Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000-2004

Summary of Environmental Monitoring and
Assessment Program (EMAP) Activities in

South Dakota, 20002004
By Allen J. Heakin, Kathleen M. Neitzert, and Jeffrey S. Shearer
Prepared in cooperation with the

South Dakota Department of Game, Fish and Parks and the
U.S. Environmental Protection Agency
Scientific Investigations Report 2006-5007
U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior
Gale A. Norton, Secretary
U.S. Geological Survey

P. Patrick Leahy, Acting Director
U.S. Geological Survey, Reston, Virginia: 2006
For product and ordering information:

World Wide Web: http://www.usgs.gov/pubprod
Telephone: 1-888-ASK-USGS
For more information on the USGS--the Federal source for science about the Earth, its natural and living resources,
natural hazards, and the environment:
World Wide Web: http://www.usgs.gov
Telephone: 1-888-ASK-USGS
Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the
U.S. Government.
Although this report is in the public domain, permission must be secured from the individual copyright owners to
reproduce any copyrighted materials contained within this report.
Suggested citation:
Heakin, A.J., Neitzert, K.M., and Shearer, J.S., 2006, Summary of Environmental Monitoring and Assessment
Program (EMAP) activities in South Dakota, 20002004: U.S. Geological Survey Scientific Investigations
Report 20065007, 45p.
iii
Contents
Abstract............................................................................................................................................................1
Introduction.....................................................................................................................................................2
Purpose and Scope...............................................................................................................................2
Acknowledgments.................................................................................................................................2
Overview of the Environmental Monitoring and Assessment Program................................................3
EMAP Implementation in South Dakota.............................................................................................3
Randomly Selected Sites.............................................................................................................4
Candidate Reference Sites.........................................................................................................4
Availability of Data Sets........................................................................................................................7
Methods and Activities................................................................................................................................15
Methods for Characterization of Physical Stream Attributes......................................................15
Reach Layout...............................................................................................................................15
Channel Dimensions and Bank Characteristics....................................................................15
Thalweg Measurements............................................................................................................16
Substrate Size and Type............................................................................................................16
Riparian Vegetation Cover and Structure...............................................................................17
Streamflow...................................................................................................................................17
Stream Gradient..........................................................................................................................18
Methods for Collecting Vertebrate Data..........................................................................................18
Seining ..........................................................................................................................................19
Electrofishing...............................................................................................................................19
Methods for Collecting Invertebrate Data.......................................................................................19
Benthic Macroinvertebrates....................................................................................................20
Periphyton....................................................................................................................................20
Methods for Assessing Water Quality.............................................................................................21
Quality Assurance and Quality Control...................................................................................21
Field Measurements...................................................................................................................21
Chemical Analysis......................................................................................................................22
Methods for Characterizing Geologic Influences on Stream Condition.....................................22
Geologic Influences on Stream Condition................................................................................................22
Basin Characteristics and Streamflow............................................................................................22
Water Quality........................................................................................................................................24
Vertebrate Richness............................................................................................................................24
Physical Habitat...................................................................................................................................24
Vertebrate /Physical Habitat Associations......................................................................................29
Summary........................................................................................................................................................29
References.....................................................................................................................................................30
Supplemental Information...........................................................................................................................33
iv
Figures
13. Maps showing:
1. Location of South Dakota EMAP randomly selected wadeable stream sites
visited during 20002003........................................................................................................5
2. Location of South Dakota EMAP candidate reference sites visited during
20022004.................................................................................................................................6
3. Generalized geologic map showing surfical geology of a part of the White
River Basin and location of multiple assessment sites in the study area...................14
4. Photograph showing field data were recorded on standardized field data sheets
during field activities............................................................................................................15
5. Diagram showing depiction of a stream reach layout..........................................................16
613. Photographs showing:
6. Field crew members laying out a transect.......................................................................17
7. Field crew members measured the wetted stream width to determine
channel dimensions throughout the designated stream assessment reach.............17
8. A field crew member making a stream discharge measurement at the
X-site...................................................................................................................................18
9. Field crew biologists documented abnormalities visible on vertebrate
specimens..............................................................................................................................18
10. Vertebrate specimens, such as this Shorthead Redhorse, were measured
following the collection and identification process.......................................................19
11. Field crew members identified vertebrate species while electrofishing.................19
12. Field crew members processing benthic macro-invertebrates.................................20
13. Crew members calibrated water-quality instruments prior to collecting
field measurements..............................................................................................................21
1415. Graphs showing:
14. Variations in annual, monthly, and daily mean streamflow for
station 06446700, Bear-in-the-Lodge Creek near Wanblee, SD, water
years 19952003....................................................................................................................25
15. Variations in annual, monthly, and daily mean streamflow for
station 06447230, Black Pipe Creek near Belvidere, SD,
water years 19932003........................................................................................................26
1618. Photographs showing:
16. Examples of fish caught, identified, and measured at Bear-in-the-Lodge
or Black Pipe Creeks include (A) channel catfish and (B) river carp sucker.............27
17. Bear-in-the-Lodge Creek, assessment sites: (A) upper site (site 1),
(B) middle site (site 3), and (C) lower site (site 4)............................................................28
18. Upper Black Pipe Creek, assessment sites: (A) upper site (site 5),
(B) middle site (site 6), and (C) lower site (site 8)............................................................28

Tables
1. Stream assessment site information for South Dakota EMAP sites visited during
20002004........................................................................................................................................8
2. Information for sites used to characterize geologic influences..........................................23
3. General guidelines for consideration in selection of candidate reference sites.............34
4. Data reporting criteria for water chemistry analyses...........................................................35
5. Analytical methodologies for water chemistry.......................................................................36
6. Water-quality data for sites on Bear-in-the-Lodge and Black Pipe Creeks......................38
7. Vertebrate information for Bear-in-the-Lodge Creek............................................................39
8. Vertebrate information for Black Pipe Creek..........................................................................40
9. Physical habitat data for sites on Bear-in-the-Lodge Creek................................................41
10. Physical habitat data for sites on Black Pipe Creek..............................................................43
11. Rapid habitat assessment ratings for sites on Bear-in-the-Lodge and Black Pipe
Creeks............................................................................................................................................45
Conversion Factors and Datums

Multiply By To obtain
Length
inch (in.) 2.54 centimeter (cm)
inch (in.) 25.4 millimeter (mm)
foot (ft) 0.3048 meter (m)
mile (mi) 1.609 kilometer (km)
Area
square foot (ft2) 929.0 square centimeter (cm2)
square foot (ft2) 0.09290 square meter (m2)
square mile (mi2) 259.0 hectare (ha)
square mile (mi2) 2.590 square kilometer (km2)
Flow rate
cubic foot per second (ft3/s) 0.02832 cubic meter per second (m3/s)
Temperature in degrees Celsius (C) may be converted to degrees Fahrenheit (F) as follows:
F=(1.8C)+32
Temperature in degrees Fahrenheit (F) may be converted to degrees Celsius (C) as follows:
C=(F-32)/1.8
Vertical coordinate information is referenced to the North Geodetic Vertical Datum of 1929
(NGVD 88).
Horizontal coordinate information is referenced to the North American Datum of 1927 (NAD 27).
vi
Other abbreviations and acronyms used:

L liters
mL milliliters
S/cm microsiemens per centimeter at 25 degrees Celsius
m micron
DENR South Dakota Department of Environment and Natural Resources
EMAP Environmental Monitoring and Assessment Program
EMAP-West Environmental Monitoring and Assessment Program-West
GF&P South Dakota Department of Game, Fish and Parks
GPS Global Positioning System
NERL National Exposure Research Laboratory
NHEERL National Health and Environmental Effects Research Laboratory
USEPA U.S. Environmental Protection Agency
USGS U.S. Geological Survey
WED Western Ecology Division
Summary of Environmental Monitoring and Assessment
Program (EMAP) Activities in South Dakota, 20002004
By Allen Heakin1, Kathleen M. Neitzert1, and Jeffrey S. Shearer2
Abstract Relatively early in the EMAP-West stream-assessment

process, it became apparent that for some streams in south-
The U.S. Environmental Protection Agency (USEPA) central South Dakota, in-stream conditions varied consid-
initiated data-collection activities for the Environmental erably over relatively short distances of only a few miles.
Monitoring and Assessment Program-West (EMAP-West) in These changes appeared to be a result of geomorphic changes
South Dakota during 2000. The objectives of the study were associated with changes in the underlying geology. For these
to develop the monitoring tools necessary to produce unbiased streams, moving stream assessment sites short distances
estimates of the ecological condition of surface waters across upstream or downstream had the potential to provide substan-
a large geographic area of the western United States, and to tially different bioassessment data. In order to obtain a better
demonstrate the effectiveness of those tools in a large-scale understanding of how geology influences stream conditions,
assessment. two streams located in south-central South Dakota were
In 2001, the U.S. Geological Survey (USGS) and the chosen for multiple stream sampling at sites located along
South Dakota Department of Game, Fish and Parks (GF&P) their longitudinal profile at points where notable changes in
established a cooperative agreement and assumed responsibil- geomorphology were observed. Subsequently, three sites on
ity for completing the remaining assessments for the peren- Bear-in-the-Lodge Creek and three sites on Black Pipe Creek
nial, wadable streams of the EMAP-West in the State. Stream were selected for multiple stream sampling using EMAP-West
assessment sites were divided into two broad categoriesthe protocols so that more could be learned about geologic influ-
first category of sites was randomly selected and assigned by ences on stream conditions.
the USEPA for South Dakota. The second category consisted Values for dissolved oxygen and specific conductance
of sites that were specifically selected because they appeared generally increased from upstream to downstream locations
to have reasonable potential for representing the best avail- on Bear-in-the-Lodge Creek. Values for pH and water tem-
able physical, chemical, and biological conditions in the State. perature generally decreased from upstream to downstream
These sites comprise the second category of assessment sites locations. Decreasing water temperature could be indicative of
and were called reference sites and were selected following ground-water inflows.
a detailed evaluation process. Candidate reference site data Values for dissolved oxygen, pH, and water temperature
will serve as a standard or benchmark for assessing the overall generally increased from upstream to downstream locations
ecological condition of the randomly selected sites. on Black Pipe Creek. The increase in temperature at the
During 2000, the USEPA completed 22 statewide stream lower sites is a result of less dense riparian cover, and the
assessments in South Dakota. During 20012003, the USGS warmer water also could account for the lower concentra-
and GF&P completed another 42 stream assessments bring- tions of dissolved oxygen found in the lower reaches of Black
ing the total of randomly selected stream assessments within Pipe Creek. Values for specific conductance were more than
South Dakota to 64. In addition, 18 repeat assessments three times greater at the lower site (1,342microsiemens per
designed to meet established quality-assurance/quality-control centimeter(S/cm)) than at the upper site (434S/cm). The
requirements were completed at 12 of these 64 sites. During increase probably occurs when the stream transitions from
20022004, the USGS in cooperation with GF&P completed contacting the underlying Arikaree Formation to contacting
stream assessments at 45 candidate reference sites. Thus, the underlying Pierre Shale.
109sites had stream assessments completed in South Dakota Vertebrate richness was found to be slightly higher for
for EMAP-West (20002004). Bear-in-the-Lodge Creek than for Black Pipe Creek. On aver-
age, reaches on Bear-in-the-Lodge Creek had a deeper thalweg
and wider wetted stream width than Black Pipe Creek. This
resulted in a larger habitat volume of aquatic vertebrates in
1
U.S. Geological Survey Bear-in-the-Lodge Creek than in Black Pipe Creek and prob-
2
South Dakota Department of Game, Fish and Parks.
Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 20002004
ably is the reason for the slightly higher vertebrate richness using rafts. During 2000, USEPA employed contractors to
found in Bear-in-the-Lodge Creek. collect data on wadeable streams. In 2001, the South Dakota
Average substrate size decreased in a downstream direc- Department of Game, Fish and Parks (GF&P) assumed the
tion for Bear-in-the-Lodge Creek. In-stream fish cover also responsibility for overseeing Environmental Monitoring
transitioned from woody debris to macrophytes in a down- and Assessment Program (EMAP) activities that focused on
stream direction for Bear-in-the-Lodge Creek, whereas the wadable streams. GF&P subsequently initiated a cooperative
predominate riparian cover transitioned from trees to barren agreement with the U.S. Geological Survey (USGS) to con-
dirt in the lower reaches. The stream channel for Bear-in-the- duct the remaining assessments.
Lodge Creek largely consisted of riffles in the upper stream Through EMAP, USEPA, USGS, and GF&P have gained
reaches and transitioned into glide or glide/riffle combinations valuable information collected in a consistent manner that
in the lower reaches. Rapid habitat assessments metrics gener- can be used to more accurately assess the condition of our
ally were scored as good except for sediment deposition and Nations and South Dakotas aquatic resources. Furthermore,
riffle frequency. bioassessment data obtained from EMAP may be used by
Average substrate size increased from silt to fine gravel the South Dakota Department of Environment and Natural
in a downstream direction for Black Pipe Creek. In-stream Resources (DENR) to develop a set of biocriteria for South
fish cover was composed of overhanging vegetation and algae Dakotas streams. Biocriteria are a set of narrative descriptions
in the upper reaches and transitioned to macrophytes in the or numerical values that States and Tribes can include in their
lower reaches. However, fish cover was sparse throughout water-quality standards. The standards can be used along with
all reaches. Riparian cover largely consisted of grasses and the chemical and physical data routinely collected by States
woody shrubs in the upper reaches of Black Pipe Creek and through their monitoring programs to better manage water
transitioned to grasses and bare dirt in the lower reaches. The resources (U.S. Environmental Protection Agency, 2002).
stream channel was largely a glide in the upper reaches and
transitioned to a glide/riffle in the middle reaches and to a
series of interconnected pools in the lower reach. No rapid Purpose and Scope
habitat assessments were completed for the upper reach, but
The primary purpose of this report is to provide an over-
the lower reaches were categorized as poor for most in-stream
view of EMAP activities conducted in South Dakota during
and near-stream conditions.
20002004. This report describes the activities and methods
used to conduct assessments on wadable, perennial streams
and presents information on the location of selected sites in
Introduction South Dakota. It describes procedures for accessing the data
sets, but does not provide a compilation of the exhaustive data
The Environmental Monitoring and Assessment Program- sets.
West (EMAP-West) was initiated in South Dakota in 2000 This report also presents data collected as part of a
by the U.S. Environmental Protection Agency (USEPA). The special effort during 2004 for two streams, Bear-in-the-Lodge
two primary objectives of the surface-water component of the Creek and Black Pipe Creek, located in south-central South
EMAP-West were to (1)develop the monitoring tools (biologi- Dakota. Sampling was conducted at three points along each
cal indicators, stream survey design, and estimates of refer- of these streams to demonstrate how changing geology along
ence condition) necessary to produce unbiased estimates of the the longitudinal stream profiles substantially influences
ecological condition of surface waters across a large geo- geomorphology and other associated stream conditions. Data
graphic area of the West; and (2)demonstrate the effectiveness pertaining to physical habitat, water chemistry, and vertebrate
of those tools in a large-scale assessment (U.S. Environmental assemblages are presented. In addition, existing streamflow
Protection Agency, 1998). Although not specifically defined as data available for Bear-in-the-Lodge and Black Pipe Creeks
an objective, data collected during the EMAP-West also will are summarized.
help to establish a baseline for comparisons with data obtained
from future monitoring efforts and could be used to document
changing ecological conditions resulting from changing land- Acknowledgments
use or land-management practices associated with regulatory Numerous individuals from various agencies provided
or restorative efforts. their assistance and support to the study. Specifically, Den-
Data collection for EMAP-West was generally limited to nis Unkenholz of GF&P provided considerable guidance and
perennial streams and rivers; that is, those streams that main- expertise for fish identifications. Dr. Charles Berry of USGS
tain at least minimal flow throughout all but the driest climatic coordinated the activities of several students who served on
conditions. Two primary components of EMAP-West included the field teamsmost notably, Nathan Morey, Vaugn Wassink,
assessments on wadeable streams and on larger, deeper rivers Jason Kral, and Bryan Able who collected, field-identified,
that typically cannot be waded. In South Dakota, all data col- and enumerated most of the aquatic vertebrate samples. Ryan
lection on large rivers was completed by USEPA contractors Thompson, John Clark, Kathy Converse, and Richard Hudson
Overview of the Environmental Monitoring and Assessment Program
of the USGS collected the physical habitat data. Gene Stueven water body is enhanced, thereby providing more validity and
and Pat Snyder of the DENR, and Michael Kuck of the U.S. usefulness to water-resources assessments, and a more factual
Department of Agriculture, Natural Resources Conservation representation of aquatic conditions to our Federal and State
Service, provided valuable assistance with the selection of decisionmakers.
potential candidate reference sites. The efforts of Tina Laid- Physical changes occurring in a water body, such as
law, Karl Hermann, and David Peck of the USEPA also are fluctuations in temperature and sediment concentrations, or
greatly appreciated. chemical changes, such as fluctuations in concentrations of
nutrients or trace metals, can serve as stressors and result from
both natural and anthropogenic sources. Even subtle changes
in physical or chemical conditions can stress more sensitive
Overview of the Environmental members of the aquatic community. This can cause a shift
Monitoring and Assessment Program in biological integrity that favors the less sensitive and more
tolerant aquatic organisms over those that are more sensitive
Historically, most of the data collected for USEPA to and less tolerant, thus providing the potential for lowering
evaluate the condition of our Nations surface-water resources species diversity. Generally speaking, a water body with good
have consisted of physical and chemical data, which have been biological integrity has the capacity to support a diverse and
collected by States and Tribes using many different methods. balanced community of organisms that are representative
These data have been compiled by USEPA and submitted to of the composition found in the natural habitat of the area.
Congress in biennial reports called 305b reports (for section Therefore, reliable bioassessment data are required to make
305b of the Clean Water Act). meaningful assessments of biological integrity, which in turn,
In the late 1980s, USEPA began to re-evaluate the is essential for providing accurate evaluations of the condition
methods previously used to determine the condition of the of our Nations surface-water resources.
Nations water resources. Several recommendations suggested The resource population of interest for EMAP-West was
that USEPA should collect data that could be used to evaluate all perennial streams and rivers represented in USEPAs River
environmental trends and identify potential problems in their Reach File (RF3), with the exception of the lower portions of
infancy (U.S. Environmental Protection Agency, 1987a). This the Great Rivers (the Columbia, Snake, Colorado, and Mis-
type of ecological risk assessment required development of souri Rivers). Because it was neither economically feasible nor
a core set of indicators of ecological conditions that could be practical to sample all perennial streams, USEPA developed a
incorporated into the bioassessment process. A risk assess- probability design to randomly select stream assessment sites
ment can be defined as a process of assigning magnitudes and that would be statistically representative of the surface waters
probabilities to the adverse effects of human activities (Suter, in the West. The design ensures that streams of all orders are
1993). included and that sites will be located throughout the region
During the 1990s, USEPA conducted research and of interest (Stevens and Olsen, 2004). Thus, the probability of
monitoring demonstrations through several regional studies, a stream site being selected for assessment is proportional to
including the Mid-Atlantic Highlands Streams Assessment its length times the weight assigned for its order. EMAP also
study, that helped to develop and refine many of the bioassess- incorporated a systematic sampling grid, designed to provide
ment monitoring techniques and designs used by EMAP-West a uniform spatial coverage, to ensure that each ecological
(U.S. Environmental Protection Agency, 2000). However, for resource is sampled in proportion to its geographical pres-
EMAP-West, some novel tools still had to be developed, pri- ence. By incorporating these two site selection processes into
marily to address the large environmental variability encoun- EMAP, USEPA believes it provides a valid mechanism that
tered throughout the western States (U.S. Environmental will allow for the extrapolation of results for streams within
Protection Agency, 1998). each State, and for streams in all regions that share similar
In 2000, USEPA initiated EMAP-West with the primary ecological characteristics (Larsen, 1997).
purpose of developing the tools needed to measure the status
and trends in the condition of the surface-water resources of
the western United States. Special emphasis was placed on
EMAP Implementation in South Dakota
developing a core set of biological measurements that would In 2004, DENR estimated that there were 10,298mi of
provide reliable bioassessment data for the diverse stream major rivers and streams in South Dakota, of which about
conditions found throughout the West. 7,360mi or 71percent have some sparse water-quality data
Bioassessments largely consist of surveys involving the available, largely as a result of compliance monitoring for
collection, identification, and enumeration of aquatic biota 305(b) reporting (http://www.state.sd.us/denr/document.htm).
(algae, invertebrates, and vertebrates) inhabiting a water body The GF&P and other cooperating agencies also have collected
and often include estimates of areal density and a categoriza- data related to the distribution and diversity of the States fish
tion of riparian vegetation. Current (2005) thinking is that populations, especially in larger streams and rivers. However,
when bioassessment data are combined with chemical and for numerous other smaller order streams and tributaries, little
physical data, the ability to estimate the overall condition of a
or no water quality or fish data are known to exist. Previous for two sites on Bear-in-the-Lodge Creek and for two sites on
monitoring and stream assessment activities likely did not pro- Black Pipe Creek.
vide detailed data sets collected using consistent methods. Fur- USEPA established an index period for stream assess-
thermore, the high level of effort associated with conducting ments in an attempt to reduce the effects of temporal varia-
complex data-collection activities in remote locations coupled tions at selected sites. The index period in South Dakota was
with the costs associated with sample analysis would make in- between June1 and August31, and was when most of the
depth stream assessments impractical and cost prohibitive for field work was completed during a 5-year period from 2000
the State without EMAP-West. through 2004.
In South Dakota, data were collected for two different Field data were recorded on standardized data sheets
categories of sites: (1)randomly selected sites assigned for (fig.4) developed by the USEPAs Western Ecology Division
assessment by USEPA (fig.1), and (2) candidate reference (WED) in Corvallis, Oregon. The completed data sheets were
sites that were specifically selected for assessment (fig.2). returned to WED, where they were optically scanned to facili-
During 2000, USEPA completed sampling for 22 randomly tate quick entry of the data into the USEPAs database and
selected sites (excluding repeat assessments) within South to minimize data entry errors. The WED also is responsible
Dakota. During 20012003, the USGS and GF&P completed for tabulating, reviewing, and verifying the large volume of
sampling for another 42 randomly selected sites assigned stream assessment data generated by field crews participating
by USEPA, bringing the total to 64 sites. Eighteen repeat in EMAP-West.
assessments were completed at 12 sites in accordance with
the EMAP-West quality-assurance plan (U.S. Environmental
Protection Agency, 1997b). During 20022004, the USGS and Randomly Selected Sites
GF&P also completed stream assessments for 45 candidate Once site location information for the randomly selected
reference sites. Thus, the total number of assessment sites sites had been obtained from USEPA (coordinates for latitude
in South Dakota during EMAP-West (20002004) was 109. and longitude in degrees, minutes, and seconds), the loca-
Stream names and location information for assessment sites tion of a site was plotted on a topographic map. The site was
are summarized in table 1. then field visited to confirm that the stream was representa-
Relatively early in the EMAP-West stream assessment tive of the target population (perennial and wadeable) and to
process, it became apparent that for some streams in south- determine the precise location of the site on the stream bank
central South Dakota, in-stream conditions varied consider- using maps and a Global Positioning System (GPS). Later,
ably over relatively short distances of only a few miles. These a field crew returned to the site to establish the length of the
changes appeared to be a result of geomorphologic changes stream reach and to conduct the sampling. USEPA identified
associated with changes in the underlying geology. For these several alternate sites that could be substituted for assigned
streams, moving a stream assessment site short distances sites when reconnaissance visits indicated that they were
upstream or downstream had the potential to provide substan- unsafe (could not be waded), non-target, or dry, or because
tially different bioassessment data. In order to obtain a better site access permission was denied. Sometimes alternate sites
understanding of how geology influences stream conditions, were substituted because errors in the sample selection process
two streams located in south-central South Dakota were identified sample locations where no stream was present.
chosen for multiple stream sampling at sites located along These site selection errors were infrequent; however, they may
their longitudinal profile at points where notable changes in represent a portion of the resource where no assessment data
geomorphology were observed. Subsequently, three sites on are available.
Bear-in-the-Lodge Creek and three sites on Black Pipe Creek Samples were collected at 64 randomly selected sites
were selected for multiple stream sampling so that more could during 20002003 (fig.1; table1). Twelve of these sites
be learned about the geologic influences on stream conditions were selected for a total of 18 repeat assessments to provide
(fig.3). estimates of important components of variability related to
A complete set of core ecological indicators established determining current status of the target population and trend
by USEPA were measured at each stream site whenever pos- detection.
sible. The ecological indicators measured included (1)physi-
cal habitat (channel and riparian characterization), (2)in-
stream characteristics (vegetation and frequency of riffles and Candidate Reference Sites
pools), (3)aquatic vertebrate assemblages (fish, amphibians,
and crayfish), (4)periphyton assemblages (algae), (5)benthic In order to provide a means for assessing the relative
macroinvertebrate assemblages (aquatic organisms without overall ecological condition of the randomly selected sites
backbones that can be seen with the naked eye), (6)field throughout South Dakota, it was necessary to establish some
properties (water temperature, pH, dissolved oxygen, specific standard or benchmark for comparison purposes. Furthermore,
conductance, and streamflow), (7)water chemistry (major estimates of reference condition are specifically included as
ions and nutrients), and (8)fish tissue contaminants. However, part of objective 1 for the EMAP-West study design (U.S.
periphyton and macroinvertebrate samples were not collected Environmental Protection Agency, 1998). In South Dakota,
98 97
104 103 102 101 100 99
Cr L. Mi
nn
lle
er
No
Be
S010 El
Ma
rth
g Cr m
La
Riv ple
S013 Sprin
esota
For
k Gra S054 R
ri R.
South nd S021
ive
River
r
Fork S012
ssou
S025 S046 S014
Mi
S002
L.
S009 S034 S027
S040 S011
Snake
S030
Moreau River
S006
Cr
S050
S041
Big
M
45
ed
ic
Co
S062
ine
tto
nw
Cr
S056
Si o u
Cherry S022
ood
x
Be
Cr Cr
C
lle Cr
r
Cr
James
S017 l Wolf
S005 ol Turtle
MISS
Kn
Fo
O
u rc
ine
S033 ver
UR
he
dic
Ri
I
Me
S029 River
S001 S020 Sa
dn
S024 Cam
S053
El
p
er
m
Riv
Cr
Ba
S049
Cr
ttle
S042
Eas
bell C
Cr
t
r
West
44 S037 S023 Cr Sk
S043
Cr
un
Firesteel
Bad Crow k
L. Vermil
S064
li
e
Cr
Fork
Medicine S035 ck
on
R
nn
S026 Cr Ro
ye
S016
e
River
S039
Ch
Cr
Ri
S038 White
Cr
En
emy
ve
RIV
r
S018 S061 S004 S057

Fork
ER
S048
Bear
S055
Ver
S008
Black Pipe Cr
Cr
er
W
S032
-in-
o
mil
S065 S007 Dry Cr
t he
Riv
tte S063
lion
-L
S051 la
River
od
unded
S019 S052 Ke P
S060 R
ge
Ho ya
Kn
S031
os
e
Wh Cr
ee
se
Cr r it e Li Pah
a S036 S028
hit
C
ebu
S044 ttl S003
Choteau
r
e
Cl
Cr
h e ad
Antelope
Riv S047
ay
Cr
er S015
Cr d Cr
Ha
Sprin
ule
Cr
Riv
t Lake Cr
g
S045
Cr
S059
Br
43
er
Cr
Base from U.S. Geological Survey digital data, 1:100,000, 19791994
Universal Transverse Mercator projection zones 13 and 14
EXPLANATION
Omernik level III ecoregions (Omernik, 1987)
0 20 40 60 MILES
Major Minor
Northwestern Glaciated Plains Nebraska Sandhills 0 20 40 60 KILOMETERS
Northwestern Great Plains Western Corn Belt Plains
Middle Rockies Lake Agassiz Plain
Northern Glaciated Plains Western High Plains
S061 Site randomly selectedNumber is site number
Figure 1. Location of South Dakota EMAP randomly selected wadeable stream sites visited during 20002003.
98 97
104 101 100 99
103 102 Cr L. Mi
nn
lle
er
No El
Be
Ma
rth Cr m
La
Riv ple
g
Sprin
esota
For
k Gra S131 R
ri R.
South nd
ive
River S115
r
Fork
S098
ssou
S124 S120 S109 S116
S087
Mi
S117
L.
S110
S088
Snake
Moreau River
Cr
S126
Big
M
45
ed
Co
ici
S099
ne
tto
nw
Cr
S101
Si o u
Cherry
ood
x
Be
Cr Cr
C
lle Cr S104
r
Cr
James
l l Wolf
no Turtle S100
MISS
S123 K
Fo
O
u
r
rc
ine
ive
UR
he
S089
dic
R
I
Me
River
S
S111
an
Cam d
El
er
pb
S130
m
Riv
Cr
Ba
Cr
ttle
Eas
Cr
t
ell Cr
West
44 S103 Cr Sk
Cr
un
Firesteel
Bad Crow k
L. Vermil
li
e
Cr
Fork
Medicine on S102
ck R
nn
Ri Cr
ve Ro
ye
r
e
Ch
S121 S125
Ri
Cr
En S112Cr
emy
ve
RIV
r
S106 S129
Be
te S092
Fork
a
S122 S093
ER
r
hi
-
S127
Ver
i
W
n
Black Pipe Cr
S118 Cr
er
W
-
S091
o
mil
S108 Dry Cr S113 S097

te
t he
Riv
at
lion
-L
Pl
S105
River
od
unded
S119 R Key
ge
Ho a
Kn
os
e
Wh Cr
ee
se
Cr r it
Pah
e Li a
hit
C
ebu
ttl
Choteau
r
e
Cl
Cr
h e ad
S114
Antelope
Riv
ay
Cr
S107 er
Cr d Cr
S128
ule
Ha
Sprin
Cr
S090
Riv
t Lake Cr
Cr
g
Br
43
er
Cr S095
Base from U.S. Geological Survey digital data, 1:100,000, 19791994
S094 S096
Universal Transverse Mercator projection zones 13 and 14
EXPLANATION
Omernik level III ecoregions (Omernik, 1987)
Major Minor 0 20 40 60 MILES
Northwestern Glaciated Plains Nebraska Sandhills 0 20 40 60 KILOMETERS
Northwestern Great Plains Western Corn Belt Plains
Middle Rockies Lake Agassiz Plain
Northern Glaciated Plains Western High Plains
S114 Candidate reference site Number is site number
Figure 2. Location of South Dakota EMAP candidate reference sites visited during 20022004.
this objective was accomplished by establishing a network In 2004, USEPA provided USGS and GF&P with a list
of candidate reference sites. These sites were selected for of additional candidate reference sites for assessment. The
assessment after preliminary field reconnaissance, when it was USEPAs list of candidate reference sites was generated with
determined that they appeared to meet an established set of a screening approach using Geographic Information System
selection criteria, and appeared to have reasonable potential Technology, aerial photograph interpretation, and validation
for representing the best available physical, chemical, and by field visits or best professional judgment. By the end of
biological conditions within each of the four major Omernik the 2004 field season, South Dakotas candidate reference site
Level III Ecoregions (Omernik, 1987) within the State (the network totaled 45 sites and included sites selected by both
Northern Glaciated Plains, the Northwestern Glaciated Plains, methods. As assessment data are made available, USEPA,
the Northwestern Great Plains, and the Middle Rockies). GF&P, DENR, and USGS will further evaluate the data to
Basically, ecoregions can be defined as areas that share similar determine if a site remains a viable candidate for the candidate
types of ecosystems and have similar environmental resources. reference site network or if it should be removed.
Locations of the various LevelIII Ecoregions and locations of
the 45 candidate reference sites where assessments were com-
pleted are shown in figure2. Additional candidate reference Availability of Data Sets
site information is provided in table1.
During 20002004, 109 stream assessments were com-
During 20022003, USGS and GF&P primarily were
pleted in South Dakota as part of EMAP-West. After field
responsible for selecting candidate reference sites for assess-
activities were finished, field data sheets were sent to USEPA.
ment. However, assistance with site selection was provided by
The data sheets were scanned and compiled in a database
personnel from various State and Federal agencies, Tribal rep-
in preparation for analysis. However, as of the date of this
resentatives, various water-resource professionals, and other
report, some of the data sets had not been verified and were
interested parties. Potential candidate candidate reference sites
not available. Eventually, all the data sets will be archived in
were screened using criteria developed and agreed upon by
the USEPAs STOrage and RETrieval (STORET) database at
representatives from the various agencies listed above. The
http://www.epa.gov/storet. The EMAP Web site at http://www.
list of candidate reference site screening criteria is provided in
epa.gov/emap/html/dataI/index.html also contains a list of
table3 in the Supplemental Information section at the end of
individuals that should be consulted prior to attempting data
the report.
retrieval and acquisition. The USEPA currently (2005) is final-
Once a list of viable candidate reference sites was created
izing a report containing statistical summaries of the data sets
using the screening criteria, sites were field visited by a team
that include an initial assessment of ecological condition for
of hydrologists and further evaluated using a field question-
the entire United States. Plans also are underway to provide a
naire. Candidate reference sites that passed the field screening
more focused report that describes the data collected specifi-
were ranked by score and the sites with the highest scores
cally for streams in the States comprising USEPA RegionVIII.
were added to the site list, and those sites with lower scores
were added to the list of alternate sites.
Table 1. Stream assessment site information for South Dakota EMAP sites visited during 20002004.
[EMAP, Environmental Monitoring and Assessment Program]
Site
number Latitude Longitude Date(s) visited
(number
refers to
fig. 1 or (degrees, minutes,
fig. 2) Sample ID Site name seconds) County Visit 1 Visit 2 Visit 3 Visit 4
Randomly selected sites sampled 20002003
S001 WSDP99-0502 Whitewood Creek EMAP site near Englewood, SD 441716 1034727 Lawrence 07-18-00 07-18-03
S002 WSDP99-0503 High Bank Creek EMAP site near Timber Lake, SD 453416 1010059 Corson 07-20-00 07-30-00 06-14-01 07-19-01
S003 WSDP99-0507 Sand Creek EMAP site below Keyapaha, SD 430708 1000604 Tripp 07-30-00 07-02-03
S004 WSDP99-0508 White Thunder Creek EMAP site near Bad Nation, SD 434118 1002612 Mellette 07-16-00
S005 WSDP99-0509 Hay Creek EMAP site near Belle Fourche, SD 443856 1035414 Butte 07-09-00 06-11-03
S006 WSDP99-0510 Moreau River EMAP site near Dewey County line in SD 451200 1013025 Ziebach 06-04-03
S007 WSDP99-0512 Platte Creek EMAP site above Platte, SD 432449 0985239 Charles 07-31-00 06-24-03
Mix
S008 WSDP99-0514 Eagle Nest Creek EMAP site near Wanblee, SD 433231 1014305 Jackson 07-15-00 06-16-03
S009 WSDP99-0515 Lone Tree Creek EMAP site near Bison, SD 452532 1022100 Perkins 07-06-00
S010 WSDP99-0516 Spring Creek EMAP site near Pollock, SD 455120 1001251 Campbell 07-06-00 06-25-03
S011 WSDP99-0525 Antelope Creek EMAP site near Date, SD 451836 1024113 Perkins 07-07-00 05-03-03
S012 WSDP99-0526 Grand River EMAP site above Black Horse Butte Creek, SD 454114 1015021 Corson 06-27-02
S013 WSDP99-0543 Stink Creek EMAP site near Bullhead, SD 454749 1011134 Corson 06-05-03
S014 WSDP99-0544 No Name Creek EMAP site near Wilmot, SD 452745 0965621 Roberts 07-01-03
S015 WSDP99-0546 Ponca Creek EMAP site near Herrick, SD 430258 0991052 Gregory 08-12-03
S016 WSDP99-0547 White River EMAP site near Okaton, SD 434546 1005003 Mellette 07-16-00 08-12-03
S017 WSDP99-0548 Belle Fourche River EMAP site above Belle Fourche, SD 444333 1035811 Butte 06-12-03
S018 WSDP99-0561 Beaver Creek EMAP site near Norbeck Lake in SD 433504 1032747 Custer 06-29-00 07-17-03
S019 WSDP99-0579 White River EMAP site near Redshirt, SD 431714 1024903 Shannon 09-04-01
S020 WSDP99-0580 Elk Creek EMAP site near Nemo, SD 441636 1033944 Lawrence 06-08-01
S021 WSDP99-0581 Louse Creek EMAP site near Timber Lake, SD 454033 1012757 Corson 07-18-01
S022 WSDP99-0582 Dupree Creek EMAP site near Carlin Flat, SD 444458 1011834 Ziebach 06-26-01
Table 1. Stream assessment site information for South Dakota EMAP sites visited during 20002004.Continued
Site Latitude Longitude Date(s) visited

number
(number
refers to
Randomly selected sites sampled 20002003Continued
S023 WSDP99-0585 Spring Creek EMAP site near Rapid City, SD 435915 1031931 Penning- 06-19-01
ton
S024 WSDP99-0586 Elk Creek EMAP site above Elm Springs, SD 441459 1023830 Meade 06-21-01
S025 WSDP99-0587 South Fork of Grand River EMAP site near Buffalo, SD 453412 1033702 Harding 06-12-01
S026 WSDP99-0588 Smith Creek EMAP site near Kimball, SD 435353 0990210 Brule 07-13-01
S027 WSDP99-0589 Mud Creek EMAP site near Groton, SD 452419 0980332 Brown 07-12-01
S028 WSDP99-0590 Turkey Ridge Creek EMAP site near Centerville, SD 430820 0970034 Turner 07-11-01 07-26-01 07-11-02 07-25-02
S029 WSDP99-0593 Alkali Creek EMAP site near Sturgis, SD 442309 1031643 Meade 06-07-01
S030 WSDP99-0594 Thunder Butte Creek EMAP site near Thunder Butte, SD 451656 1015542 Ziebach 06-26-01
S031 WSDP99-0596 Whetstone Creek EMAP site near Bonesteel, SD 431047 0990235 Gregory 08-03-01
S032 WSDP99-0599 White River EMAP site near Rockyford, SD 432903 1023039 Shannon 06-19-02
S033 WSDP99-0602 Bear Butte Creek EMAP site near Sturgis, SD 442829 1031312 Meade 06-11-01
S034 WSDP99-0603 Unnamed Creek EMAP site near Timber Lake, SD 453033 1010505 Corson 07-17-01
S035 WSDP99-0604 Big Creek EMAP site near Oacoma, SD 434920 0992704 Lyman 07-10-01
S036 WSDP99-0605 Ponca Creek EMAP site near Burke, SD 430919 0992156 Gregory 07-25-01
S037 WSDP99-0657 Spring Creek EMAP site below Sheridan Lake in SD 435914 1032505 Penning- 06-05-02
ton
S038 WSDP99-0658 White River EMAP site near Jackson County line in SD 434148 1020949 Shannon 06-17-03
S039 WSDP99-0660 Cottonwood Creek EMAP site near Presho, SD 434038 1000530 Tripp 07-10-02
S040 WSDP99-0664 North Fork of Moreau River EMAP site, SD 452012 1032039 Harding 06-26-02
S041 WSDP99-0665 Moreau River EMAP site, SD 450914 1023548 Perkins 06-25-02
S042 WSDP99-0666 Bad River EMAP site near Capa, SD 440646 1005702 Jones 07-09-02
S043 WSDP99-0667 Pipestone Creek EMAP site near Minnesota border in SD 435110 0963041 Moody 07-23-02
S044 WSDP99-0669 Hat Creek EMAP site near Rumford, SD 430803 1033752 Fall River 06-06-02 06-18-02 06-10-03 08-13-03
S045 WSDP99-0670 Spring Creek EMAP site above Little White River in SD 430509 1010225 Todd 07-12-02

number
(number
refers to
Randomly selected sites sampled 20002003Continued
S046 WSDP99-0672 Grand River EMAP site below Black Horse Butte Creek, SD 453957 1014214 Corson 06-12-02
S047 WSDP99-0674 Beaver Creek EMAP site above Beaver Lake in SD 430110 0972730 Yankton 07-24-02
S048 WSDP99-0678 Little White River EMAP site at White River, SD 433415 1004545 Mellette 07-18-02
S049 WSDP99-0679 Bad River EMAP site at Capa, SD 440624 1005814 Jones 07-09-02
S050 WSDP99-0681 Moreau River EMAP site near Imogene, SD 450812 1024848 Perkins 06-13-02
S051 WSDP99-0695 Cheyenne River EMAP site, 1.5 mile east of Edgemont, SD 431849 1034712 Fall River 06-18-02
S052 WSDP99-0696 Little White River EMAP site near Soldier Creek, SD 432000 1005323 Todd 07-17-02
S053 WSDP99-0697 Elk Creek EMAP site near Bend, SD 441459 1031022 Meade 06-04-02
S054 WSDP99-0698 White Shirt Creek EMAP site near McIntosh, SD 454615 1011636 Corson 06-11-02
S055 WSDP99-0501 Medicine Root Creek EMAP site below Kyle, SD 433149 1021355 Shannon 07-11-00
S056 WSDP99-0505 Cobb Creek EMAP site near Brandt, SD 444148 0963351 Deuel 06-28-00
S057 WSDP99-0506 Wolf Creek EMAP site near Bridgewater, SD 433015 0973229 McCook 06-30-00
S059 WSDP99-0521 Bull Creek EMAP site above SD-NE State line in SD 430110 1005205 Todd 07-25-00
S060 WSDP99-0522 Porcupine Creek EMAP site at Sharps Corner, SD 432256 1022320 Shannon 07-11-00
S061 WSDP99-0523 Eagle Nest Creek EMAP site near Wanblee, SD 433837 1014659 Jackson 07-13-00
S062 WSDP99-0527 Artichoke Creek EMAP site at Missouri River near Agar, SD 445353 1002118 Sully 07-22-00
S063 WSDP99-0533 Turkey Ridge Creek EMAP site near Turkey Ridge, SD 431540 0971503 Turner 06-28-00
S064 WSDP99-0540 Spring Creek EMAP site below Rockerville, SD 435611 1030914 Penning- 07-06-00
ton
S065 WSDP99-0541 Bear-in-the-Lodge Creek EMAP site near Potato Creek, SD 433140 1014749 Jackson 07-14-00
10 Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 20002004
Candidate reference sites sampled 20022004

S087 WSDP02-R001 Firesteel Creek EMAP reference site near Firesteel, SD 453147 1011921 Corson 07-23-02
S088 WSDP02-R002 Swan Creek EMAP reference site near Akasaka, SD 451923 1001137 Walworth 07-24-02

number
(number
refers to
Candidate reference sites sampled 20022004Continued
S089 WSDP02-R003 Medicine Knoll Creek EMAP reference site near Canning, 442632 1000001 Hughes 07-25-02
SD
S090 WSDP02-R004 Rock Creek EMAP reference site near Valentine, NE 430516 1003214 Todd 07-31-02
S091 WSDP02-R005 Bear-in-the-Lodge Creek EMAP reference site near Wanblee, 433226 1014832 Jackson 07-30-02
SD
S092 WSDP02-R006 East Fork Vermillion River EMAP reference site near Mon- 432932 0970938 Turner 08-01-02
roe, SD
S093 WSDP02-R007 Twelvemile Creek EMAP reference site near Ethan, SD 433148 0975546 Hanson 08-02-02
S094 WSDP02-R008 Spring Creek EMAP reference site near Greenwood, SD 425421 0981520 Charles 08-06-02
Mix
S095 WSDP02-R009 Choteau Creek EMAP reference site near Avon, SD 425402 0980702 Charles 08-06-02
Mix
S096 WSDP02-R010 Emanuel Creek EMAP reference site near Springfield, SD 425133 0975638 Bon 08-07-02
Homme
S097 WSDP02-R011 Peterson Creek EMAP reference site near Canton, SD 432053 0963236 Lincoln 08-08-02
S098 WSDP02-R012 Chekapa Creek EMAP reference site near Grenville, SD 453051 0971329 Roberts 08-13-02
S099 WSDP02-R013 West Fork Lac qui Parle River EMAP reference site near 444700 0962813 Deuel 08-14-02
Gary, SD
S100 WSDP02-R014 Peg Munky Run EMAP reference site near Estelline, SD 443455 0964812 Deuel 08-14-02
S101 WSDP02-R015 Stray Horse Creek EMAP reference site near Castlewood, SD 444402 0965709 Hamlin 08-14-02
S102 WSDP02-R016 West Pipestone Creek EMAP reference site near Sherman, 434522 0963256 Minneha- 08-16-02
SD ha
S103 WSDP03-R017 Castle Creek EMAP reference site near Deerfield Lake in SD 440230 1035156 Penning- 07-07-03
ton
S104 WSDP03-R018 Turtle Creek EMAP reference site near confluence at Wolf 444313 0983743 Spink 07-16-03
Creek in SD
S105 WSDP03-R019 Turkey Ridge Creek EMAP reference site near Turkey Ridge, 431530 0971428 Turner 07-31-03
SD
Overview of the Environmental Monitoring and Assessment Program 11

number
(number
refers to
S106 WSDP03-R020 Pass Creek EMAP reference site near Hwy 44 in SD 433801 1012723 Jackson 07-08-03
S107 WSDP03-R021 Lake Creek EMAP reference site near Lacreek National 430448 1014004 Bennett 08-05-03
Wildlife Refuge in SD
S108 WSDP03-R022 Blackpipe Creek EMAP reference site near Hwy63 in SD 433005 1011200 Mellette 07-10-03
S109 WSDP03-R023 Blackhorse Butte Creek EMAP reference site near Meadow, 453350 1015527 Corson 07-22-03
SD
S110 WSDP03-R025 Owens Creek EMAP reference site near Ortley, SD 452055 0971232 Roberts 07-24-03
S111 WSDP03-R026 Cain Creek EMAP reference site near confluence at James 441552 0981155 Beadle 07-15-03
River in SD
S112 WSDP03-R027 Enemy Creek EMAP reference site below Mitchell, SD 433743 0980217 Davison 07-17-03
S113 WSDP03-R028 Wolf Creek EMAP reference site near Wolf Creek Colony, 432305 0973620 Hutchin- 07-30-03
SD son
S114 WSDP03-R029 Keya Paha River EMAP reference site near Hidden Timber, 431130 1001859 Todd 08-06-03
SD
S115 WSDP03-R032 Elm Creek EMAP reference site near Westport, SD 454002 0983111 Brown 07-29-03
S116 WSDP04-R033 High Bank Creek EMAP reference site near Little Eagle, SD 453733 1005426 Corson 06-22-04
S117 WSDP04-R034 Clarks Fork Creek EMAP reference site near Buffalo, SD 453256 1032255 Harding 06-03-04
S118 WSDP04-R035 Little White River EMAP reference site south Hwy 44 near 432851 1004548 Mellette 07-08-04
White River, SD
S119 WSDP04-R036 Little White River EMAP reference site at Ghost Hawk Park, 431554 1005402 Todd 07-06-04
near Rosebud, SD
S120 WSDP04-R038 South Fork Grand River EMAP reference site near Buffalo, 453707 1032031 Harding 06-02-04
SD
S121 WSDP04-R040 Eagle Nest Creek EMAP reference site near Interior, SD 434049 1014644 Jackson 06-14-04
S122 WSDP04-R041 Black Pipe Creek EMAP reference site north Hwy 44 near 433822 1011255 Mellette 06-09-04
Norris, SD
S123 WSDP04-R044 Plum Creek EMAP reference site near Cherry Creek, SD 443559 1012744 Haakon 06-21-04
Site
number Latitude Longitude Date(s) visited
(number
refers to
S124 WSDP04-R045 South Fork Grand River EMAP reference site above Buffalo, 453324 1033944 Harding 06-04-04
SD
S125 WSDP04-R046 Pass Creek EMAP reference site near Kadoka, SD 434126 1012807 Jackson 06-07-04
S126 WSDP04-R047 South Fork Moreau River EMAP reference site below Zeona, 450801 1025030 Perkins 06-01-04
SD
S127 WSDP04-R048 Bear-in-the-Lodge Creek EMAP reference site below Wan- 433338 1014821 Jackson 06-05-04
blee, SD
S128 WSDP04-R049 Little White River EMAP reference site near Spring Creek, 430631 1010613 Todd 07-07-04
SD
S129 WSDP04-R050 West Fork Vermillion River EMAP reference site near Stan- 433240 0972115 McCook 07-09-04
ley Corner, SD
S130 WSDP04-R051 Flandreau Creek EMAP reference site near Flandreau, SD 440428 0962754 Moody 07-01-04
S131 WSDP04-R052 Oak Creek EMAP reference site near Mahto, SD 454406 1003654 Corson 06-23-04
Overview of the Environmental Monitoring and Assessment Program 13
10215' 10200' 10145 10130 10115' 10100' 10045'

Kfh
4400'
PENNINGTON COUNTY JACKSON COUNTY
Kp
Tw Kp
Qe Kfh
Qt
JONES COUNTY
Qal Qt
Qt
River
8
7
Red Sto
Kp
Tw
Black
4345' Qe
Kp Qe
White
Pass
ne
Qal
Pipe
Cre
4
Cra
Tw
er
ek
2004 EMAP
6 reference site Riv
ven
Lon
Eag
Cre
Qe
gC
Cr
Kp
le N
ek
2004 EMAP
eek
ree
Creek
3
Me
reference site
k
st
2
dic
Qt
Cr
Tw
ine
eek
Tg
1 Ta Qc
4330'
Bea
5
Roo
r-
in-
Tw
t
MELLETTE COUNTY
the
-l o
Tg ge JACKSON COUNTY
d
To
Ta
Cr
SHANNON COUNTY
eek
Cree
Ta
Por
te
To
k
c
upi
Whi
4315' To
ne
Cr
ee
k
Qe
Qe
Ta Lit
Tb tle
Qt Qe
BENNETT COUNTY TODD COUNTY
Base from U.S. Geolgoical Survey digital data 1:100,000 Geology modified from Martin and others, 1:500,000, 2004
Kadoka, 1980, Martin, 1983, Mission, 1982, and Wall, 1981
Universal Transverse Mercator projection, zone 13 0 10 20 MILES
0 10 20 KILOMETERS
EXPLANATION
Surficial geology Stream assessment sites
Quaternary units 2 Continuous-record streamflow-gaging station
Qal Alluvium Number indicates site number (table 2)
Qc Colluvium 1 Surface-water-quality sampling siteNumber
Qe Eolian deposits indicates site number (table 2)
Qt Terrace deposits
Tertiary units
Tg Gravel deposits
To Ogallala Formation (Pliocene) SOUTH DAKOTA
Tb Batesland Formation (Miocene)
Ta Arikaree Formation (Miocene) Study
Tw White River Group (Oligocene and Eocene) area
Cretaceous units
Kfh Fox Hills Sandstone (Upper Cretaceous)
Kp Pierre Shale (Upper Cretaceous)
Middle White River Basin boundary
Figure 3. Generalized geologic map showing surficial geology of a part of the White River Basin and location of multiple
assessment sites in the study area.
Methods and Activities 15
yield about 90percent of the fish species present (Reynolds

and others, 2003). Similar considerations for other factors
led to development of EMAP protocol that stream reaches
should be at least 40 channel-widths long or a minimum of
150meters(m), whichever is longer.
The randomly selected site location coordinates (latitude
and longitude) provided by USEPA were designated as the
X-site. For each stream site, the mean wetted width at the
X-site was determined and then multiplied by 40 to get the
total length of the stream reach to be assessed (fig.5). The
stream reach was then divided into 11 equally spaced tran-
sects, five upstream and five downstream from the X-site,
creating 10 segments that were each four stream-widths long
(fig.6). In cases where the wetted width of the stream at
the X-site was fairly narrow (less than 3.75m), each of the
10segments was assigned a length of 15m. Therefore, either
process produced 10 equally spaced segments separated by
Figure 4. Field data were recorded on standardized field data 11transects that were subsequently labeled from A to K. Typi-
sheets during field activities. cally, the A transect represented the most downstream transect
and K represented the most upstream transect. The middle or
Ftransect typically represented the location of the X-site.
Methods and Activities
Channel Dimensions and Bank Characteristics
This section of the report contains an overview of EMAP
methods for data collection and a description of the types At each of the 11 stream transects (labeled A to K; fig.5)
of data collected during stream assessments. Methods are the wetted width of the stream was measured and recorded on
described for characterizing physical stream attributes, col- field forms in order to determine channel dimensions present
lecting vertebrate and invertebrate data, and assessing water throughout the designated stream assessment reach (fig.7).
quality. Methods used to characterize geologic influences on Measurements of channel width allow for the determination
stream conditions also are described. of the streams structural complexity and when coupled with
depth measurements, provide a mechanism for estimating
stream volume throughout the reach.
Methods for Characterization of Physical Bank characteristics include several measurements such
Stream Attributes as estimates of bank angle, undercutting, and bankfull flow
during base-flow conditions. Bank angle is determined for
Most of the methods used for assessing stream condition both banks at each of the 11 transects. To accomplish this, a
during EMAP-West were developed during previous EMAP rod was laid on the bank with one end at the waters edge, then
studies conducted by USEPA. The methods were developed a clinometer was placed on the rod to obtain the bank angle.
jointly by investigators working at the USEPAs National Measurements of bank characteristics also include
Exposure Research Laboratory (NERL) in Cincinnati, Ohio, estimates of the extent of bank undercutting, channel incision,
and by the National Health and Environmental Effects and height of bankfull flow above the present water-surface
Research Laboratory (NHEERL) in Corvallis, Oregon. elevation. The extent of bank undercutting was determined
The methods described in this section of the report are by measuring the horizontal distance from the deepest point
taken from Peck and others (2003). A more thorough discus- of the undercut to a point on the end of the protruding over-
sion of the following methods can be found in that document. hang of the bank to where a vertical plumb line would hit the
waters surface. The length of the measured section provides
an estimate of the extent of bank undercutting.
Reach Layout An estimate of channel incision was obtained when a
One of the first tasks for characterization of physi- surveyors rod was held perpendicular to the water surface just
cal stream attributes was for the field crew to establish the at the edge of the water. Channel incision was determined to
sampling reach. To ensure that an accurate representation of be the height up from the waters surface to the first terrace of
environmental conditions and biota are obtained, a sufficient the valley floodplain. Height estimates generally were deter-
stream length needs to be sampled. Previous studies conducted mined only by sighting.
by USEPA have shown that assessing a stream reach that Estimates for the height of bankfull flow above the pres-
is equivalent to 40 channel widths in length will generally ent base-flow water level were made by placing a surveyors
rod at the waters edge while observing the physical evidence
FLOW D
C
K E
X-site L
J
I
L H F
C G C
B
R
L R C A
R C L
SAMPLING POINTS
L = Left C = Center R = Right
First point (transect A)
determined at random
Distance between transects = 4 times Subsequent points assigned
mean wetted width at X-site in order L, C, R
Total reach length = 40 times mean wetted width at X-site (minimum = 150 meters)
Figure 5. Depiction of a stream reach layout (reproduced from Environmental Monitoring and Assessment
Program-Western Pilot field manual courtesy of U.S. Environmental Protection Agency).
on the stream banks, then estimating their elevation using Thalweg Measurements
the rod. Physical evidence consisted of locating areas where
stream sediments transitioned to terrestrial vegetation. Other The term thalweg refers to the deepest portion of the
examples of physical evidence include the presence of moss stream channel. Typically, depth measurements were collected
on rocks along the bank and the presence of drift material at 100 to 150 equally spaced points throughout the reach, and
deposited along the bank and on the overhanging vegetation. the resulting data can be used to construct a thalweg profile,
After identifying areas of bankfull flow on each bank, the which provides a longitudinal representation of channel depth.
width of the stream was measured between the two points and The depth measurements also can provide valuable informa-
recorded. This allowed for calculation of stream volume at tion about stream size and channel complexity as well as the
bankfull flow. location and relative size of riffles and pools. During thalweg
measurements, the location and width of sand or gravel bars
also were noted and recorded.
The number of depth measurements and spacing between
them was based on the wetted width of the stream at each tran-
sect. At places where the pools were too deep to be waded, a
calibrated surveyors rod was rested on the bottom of the pool,
and a clinometer was laid on the rod to measure the angle of
insertion. The depth reading from the rod also was recorded.
Using those two values, a pool depth was calculated.
Substrate Size and Type

Characterization of the substrate is a critical component
of any bioassessment because the substrate size and type (silt,
sand, gravel, and cobbles) have a large influence on the com-
position and diversity of aquatic invertebrates and vertebrates
inhabiting a stream. Substrate size also has a direct influence
on both hydraulic roughness and stream velocity. Furthermore,
Figure 6. Field crew members laying out a transect. a large percentage of fine sediments can provide an indication
insects, algae, and fish. Terrestrial vegetation provides bank

stability that can reduce sediment loading. The presence of
non-native or invasive species of plants or agricultural crops
within the riparian corridor also provides a means of assessing
potential effects of anthropogenic activities.
Stream canopy cover was measured using a spherical
convex canopy densiometer. Measurements were made at
mid-channel, right edge of water, and left edge of water on all
11transects (AK). Readings were made holding the densiom-
eter 0.3m above the water surface while facing upstream, right
bank, downstream, and left bank.
Terrestrial vegetation and structure were estimated for
three conceptual layers near or above the streamthe canopy
layer consisting of vegetation greater than 5m in height, the
understory layer consisting of vegetation from 0.5to 5m in
Figure 7. Field crew members measured the wetted stream height, and the ground cover layer consisting of vegetation less
width to determine channel dimensions throughout the designated than 0.5m in height. At the mid-channel point of each tran-
stream assessment reach. sect, an area was visualized that extended 5m upstream and
5m downstream and 10m out from both stream banks. Within
these two areas, visual estimates were made to determine the
dominant vegetation type and areal extent for each of the three
of the extent that erosional processes are occurring upstream, layers. Various keys were used to assist with the identification
and sometimes can be linked to anthropogenic activities such of trees and non-native or invasive plants.
as logging, mining, and farming within the drainage basin.
To provide an accurate determination of substrate size
and type, bed materials were categorized into various classes Streamflow
and sizes according to classifications provided by the U.S.
The EMAP study design established an index period
Environmental Protection Agency (2001). Determinations of
for conducting stream assessments that roughly runs from
substrate size and type were made at five locations along each
the beginning of June through the end of August. The intent
transect (5-point pebble-counts), at points equal to 100 (right
of establishing this index period was to conduct assessments
stream bank), 75, 50, 25, and 0percent (left stream bank) of
under steady or base-flow conditions. Sampling during high-
the wetted width of the individual transect. Five-point pebble-
flow conditions likely would produce different chemical and
counts also were made at locations midway between estab-
biological data than those obtained during stable base-flow
lished transects so that data were collected from 21 transects at
conditions. Furthermore, it is difficult and potentially danger-
a total of 105 points along the stream reach.
ous to conduct assessments when the water is high and turbid.
The extent (average percent) of embeddedness also
No assessments were made when streams appeared to be
was estimated at points where substrate size and type were
approaching bankfull levels, or when streams where located in
measured, but only at transects A through K. At these points,
very remote areas where recent rainfall made access difficult.
embeddedness was estimated within the area of a circle
Visits to sites were rescheduled when unfavorable conditions
approximately 10centimeters (cm) in diameter. Embedded-
were encountered.
ness is an estimate of the extent that bed materials are buried
Streamflow was determined at most assessment sites
in bottom sediments that are the size of sand grains (0.06
(fig.8) at the Xsite coordinates provided by USEPA using
2millimeters (mm) in diameter) or smaller; thus, sands and
methods established by USGS (Rantz and others, 1982).
silts were considered to be 100-percent embedded, whereas
Streamflow at some sites could not be measured because the
bedrock and hardpan were considered to be 0-percent embed-
water level was too low to measure. For those sites, only visual
ded.
estimates of streamflow were provided. Some sites consisted
of only a series of intermittent pools of varying sizes and sub-
Riparian Vegetation Cover and Structure sequently only estimates, or no streamflow data, were reported
for those sites.
Riparian vegetation has important influences on stream
condition. Tall trees provide a canopy over the stream that pro-
vides shade and lowers water temperature. Leaves from over- Stream Gradient
hanging trees fall into the stream and become food for aquatic
The velocity of a stream is greatly influenced by stream
insects and provide a source of particulate organic material
gradient. Increases in stream gradient increase velocity,
for other organisms. Limbs from these trees also fall into the
thereby increasing the streams ability to erode and transport
stream and provide additional organic material and habitat for
repeated by moving upstream until the gradient between each

successive transect was measured. At points where there was
no direct line of site between transects, intermediate measure-
ments were made and recorded at points between transects.
Methods for Collecting Vertebrate Data

The purpose of collecting vertebrate data was to deter-
mine their relative abundance throughout the assessment reach
and to identify any obvious external abnormalities present
on the specimens (fig.9). Trained biologists from GF&P or
from South Dakota State University conducted the sampling
and identification activities. Following identification, fish
were measured, inspected, and returned to the stream as soon
as possible (fig.10). State or Federally listed species were
photographed on a measuring board next to a card containing
the stream name and date of collection, then were immediately
returned to the water. Overall, mortality rates generally were
very low. Some specimens that proved difficult to identify in
the field were sent to the Smithsonian Institution in Washing-
ton, D.C., for identification. Only amphibians and fish were
counted; reptiles were not included in the tallies. Crayfish also
were tallied when collected to provide information related to
potentially introduced species.
Voucher specimens were collected whenever possible.
These specimens will provide a permanent, archived, histori-
cal record of fish collections. After the required data were
recorded, selected specimens were anesthetized, placed in
nylon mesh bags, then put into a labeled jar containing a
formalin preservation solution. Some vouchered samples were
used for analysis of fish tissue contaminants. All vouchered
samples were shipped to the National Museum of Natural
Figure 8. A field crew member making a stream discharge History in Washington, D.C., for confirmation of identification
measurement at the X-site. and for permanent cataloging.
All areas between established transects were sampled
unless they were too deep to wade or the pools were to small
and shallow to hold any targeted organisms. Vertebrate
sediments. Changes in gradient along the longitudinal profile samples were collected using either seining or electrofishing
of a stream also enhances the diversity and complexity of the
aquatic habitat. As velocity increases, streamflow changes
from laminar to turbulent flow. The resulting turbulent flow
helps facilitate the exchange of gases between the stream and
the atmosphere.
Measurement of stream gradient was completed by a two-
person team with each person having a surveyors pole flagged
at exactly the same height. Measurements were made starting
at the downstream end of the reach and were accomplished by
backsiting. For example, one person would stand at the waters
edge at transect A while the other person would stand at the
waters edge at transect B. Team members used a clinometer
to measure the percent slope between the two transects. One
person would stand at the upstream transect and hold the cli-
nometer at the previously flagged level on their pole and back-
site to the flagged level on the downstream pole and record the
percent slope between the two points. This process would be Figure 9. Field crew biologists documented abnormalities visible
on vertebrate specimens.
Figure 10. Vertebrate specimens, such as this Shorthead Figure 11. Field crew members identified vertebrate species
Redhorse, were measured following the collection and while electrofishing.
identification process.
methods. Seining was used when streams appeared turbid, net from the middle of the stream to the left bank. A third per-
when field measurements indicated that stream conductiv- son followed behind the operator with yet another net. Netted
ity was too high for electrofishing, or when the presence of vertebrates were placed in buckets carried along by the netters
Topeka Shiners (an endangered species) was possible. in the stream and were later emptied into larger buckets posi-
tioned on shore at the next upstream transect. The fourth team
member stayed on the bank and initiated the identification and
Seining enumeration process. Shocking proceeded in a similar manner
A two-person seine with a mesh size of 0.6cm was used as seining, from downstream to upstream. Two people could
when stream conditions dictated. Seining began at the down- complete the electrofishing on small creeks and streams.
stream end of the reach (A transect) and proceeded upstream.
Riffle, pool, and snag habitats were sampled when present. As Methods for Collecting Invertebrate Data
seining progressed to the next transect upstream, the contents
of the seine were dumped into buckets and the biologists Aquatic invertebrate samples collected during EMAP-
began tallying and recording the data. This procedure was West consisted of both benthic and periphyton macroinverte-
repeated until the crew reached the final upstream (K) transect. brates. Both of these macroinvertebrates serve as very useful
indicators of aquatic condition because they tend to respond
rapidly to changing environmental conditions, often in very
Electrofishing different ways (Fore and others, 1996). The type of response
Most of the vertebrate samples were collected by sein- can sometimes be linked to a particular type of stressor such as
ing. However, a Smith-Root model 12-B, P.O.W. backpack nutrient enrichment or exposure to toxic metals, herbicides, or
electrofishing unit (DC pulsed; volts 100 to 600; pulse rate of other forms of aquatic contamination.
60 hertz and a pulse width of 2-6 milliseconds) was used at Because benthic macroinvertebrates are not very mobile,
several stream assessment sites where conductivities gener- are relatively easy to catch, and often live in the aquatic envi-
ally were low and the water was clear (fig.11). Electrofishing ronment for a year or more, they provide a convenient method
in large streams typically required the efforts of all four team for assessing the biological integrity of a stream. Therefore,
members. Team members in the stream wore waders and rub- much can be learned about the short-term history of in-stream
ber gloves to prevent being shocked. Netters were careful not conditions by looking at benthic macroinvertebrate species
to touch the water or the anode while the shocking unit was diversity and community composition.
operating. The person operating the backpack shocker often
held the anode in one hand and a dip net in the other hand
(fig.11) and typically worked a net from the middle of the
stream over to the right bank, while a second person worked a
Benthic Macroinvertebrates
The term benthic macroinvertebrate generally is used
to describe organisms that live in the bottom substrate of fresh-
water environments during part of their life cycle. For many
years, the usefulness of benthic macroinvertebrate data for
assessing stream conditions was not fully appreciated. How-
ever, recent advances associated with quantitative sampling
methods, analytical processes, taxonomy, and identification
methodology, followed by the compilation of toxicological
data related to species response to pollution, have all served
to strengthen the case for making benthic macroinvertebrate
data an integral part of biomonitoring programs. Although
the costs of collecting benthic macroinvertebrate samples are
relatively low, large numbers of organisms are needed in order
to provide more precise estimates of population abundance,
and substantial costs can be incurred as a result of sample
processing and identification (Rosenberg and Resh, 2001). Figure 12. Field crew members processing benthic macro-
The USEPA has recognized the importance of benthic macroinvertebrates.
invertebrate data for assessing stream condition and biological
integrity and has incorporated data-collection and analysis
activities into the EMAP stream assessment process (Klemm
and others, 1990). Periphyton
Two types of benthic macroinvertebrate samples were
collectedreach-wide and targeted riffle. The reach-wide Periphyton encompasses several types of aquatic organ-
samples were collected at the same time and from the same isms including algae, fungi, bacteria, protozoans, and other
locations where periphyton samples were collected. Samples organic matter. For EMAP, periphyton samples were col-
were collected using a 500-micron (m) mesh D-frame kick lected from both erosional and depositional habitats and then
net that had an opening width of 12in. The opening of the net composited into a single reach-wide sample for processing.
was placed facing upstream so that the current swept dislodged Erosional habitats consisted of rapidly flowing areas of the
organisms into the net. A 1-ft2 area directly in front of the stream such as riffles where submerged rocks or woody debris
net was visualized, and all loose rocks and substrate particles were present. Depositional habitats consisted mostly of pools
(larger than a golf ball) that were more than halfway inside where flows were diminished.
the 1-ft2 area were picked up and scrubbed with a brush so Sampling started at the most downstream (A) transect and
that any dislodged organisms were carried into the net by the proceeded upstream. The starting position on the A transect
current. Cleaned rocks were then returned to the stream bed was randomly selected from one of three positions (right
outside the 1-ft2 area in front of the net. The substrate area in bank, left bank, center channel) and alternated as sampling
front of the net was then vigorously disturbed for 30seconds progressed upstream. Thus, if the right bank was randomly
by kicking. Samples were rinsed into a bucket and composited selected for the A transect, periphyton would be collected
with reach-wide samples obtained from the other transects. from the B transect at the left bank position and from the
Targeted riffle samples were collected using methods Ctransect at the center channel position alternating until all
described for reach-wide samples. However, a minimum of 11transects were sampled (fig.5).
eight 1-ft2 areas were required for a sample to be collected. For riffle habitats, a delimeter with an inside area of
Multiple areas on a single riffle could be sampled to obtain the 12square centimeters (cm2) was placed on the upper surface
eight samples necessary in the event that the reach consisted of a rock that was completely submerged, and the area was
largely of pool-glide type habitat. All eight targeted riffle brushed with a toothbrush for about 30seconds and then the
samples were combined into a single composite sample prior scrubbed area was rinsed through a funnel into a 500milli-
to processing. liter (mL) bottle and composited. For depositional areas, the
Sample processing for reach-wide and targeted riffle delimeter was placed on the stream bed, and the top 1cm of
samples consisted of screening samples of each type through bottom material within the delimited area was sucked into a
a 500-m mesh sieve (fig.12) to remove as much debris and 60mL syringe and composited.
sediment as possible. Rinse bottles filled with stream water After sampling, a 50-mL aliquot of the composite was put
were used to facilitate this process. Samples were then rinsed into a small sealable container and preserved with a 10percent
into containers labeled as reach-wide or targeted riffle and formalin solution and labeled identification and enumeration
preserved with 95-percent ethanol. sample. Another 50mL aliquot of the composite was placed
in another small sealable container and labeled acid/alkaline
phosphatase activity, and the sample was placed on ice. A the quality-assurance plan (U.S. Environmental Protection
third aliquot consisting of 25mL of the composite sample Agency, 1997). Field team leaders also were provided with
was filtered through a glass fiber filter, and the filter and phone numbers of USEPA contacts that could provide addi-
filtrate were placed into a small sealable container and labeled tional guidance and information.
biomass sample then placed on ice. A fourth aliquot consist- Twelve sites (approximately 1520percent) were revis-
ing of 25mL of the composite sample was filtered through a ited for repeat assessments, either during the same field season
glass-fiber filter, and the filter and the filtrate were placed in or during successive field seasons, to assess the variability and
another small resealable container and labeled chlorophyll precision of the various methods used to measure ecological
sample, then put in a resealable bag and placed on ice. indicators (Larsen, 1997). Furthermore, annual field audits
were conducted by USEPA personnel during actual stream
visits, and the entire stream assessment process was evaluated
Methods for Assessing Water Quality for compliance with EMAP methods and protocols.
Two methods were used to assess stream-water quality
for EMAP-West. Field measurements were made using sub- Field Measurements
mersible multi-probe instrumentation that provided instanta-
neous in situ measurements of stream-water quality for four Field measurements were completed using submersible
properties: (1)dissolved oxygen, (2)pH, (3)specific conduc- multi-probe water-quality instruments that were calibrated
tance, and (4)water temperature. Field measurements were each time they were used (fig.13). Instrument calibration fol-
made at the approximate location of the centroid of flow at the lowed guidelines established by the manufacturer and guide-
X-site (Ftransect; fig.5). lines for field measurements outlined in the USGS National
Aliquots of stream water also were collected and sent Field Manual for the Collection of Water-Quality Data (U.S.
to WED for analysis. Water samples were collected by team Geological Survey, 19972004). All calibration data were
members wearing latex surgical gloves to prevent sample recorded in logbooks that accompanied each instrument into
contamination. Samples were collected from the centroid of the field and included the operators observations about instru-
flow and put into a 4-liter (L) acid rinsed container that was ment performance and maintenance. USGS employees with
completely filled to remove any trapped air. The container the responsibility of collecting water-quality data generally
was tightly sealed, labeled, and placed immediately on ice. receive 2weeks of intensive training at the USGS National
Samples were shipped in a cooler filled with ice to USEPA Training Center in Denver, Colorado, where they learn the
by an express service. Following receipt, the chilled water theories and methods used for the collection of ground-water
sample was filtered and preserved by USEPA, generally and surface-water samples. USGS field personnel that rou-
within 72hours of sample collection. Concentrations of trace tinely collect field measurement data that are entered into
elements, major ions, nutrients, and turbidity were measured the national database also are required to participate in the
from aliquots taken from this sample. National Field Quality Assurance Program that audits the
Additional water samples were collected in two 50mL performance of instruments and operators on at least an annual
sterile syringes that were held underwater and filled, and basis (Stanley, 1996).
then held upright while the air was ejected from the syringe.
Syringe water was used largely for the analysis of pH and
dissolved inorganic carbon. Specially designed teflon syringe
locks were used to protect samples from exchanging carbon
dioxide with the atmosphere. Filled and locked syringes were
labeled, sealed into special shipping containers, placed in the
ice chest, and sent with the other time-dependant samples to
USEPA.
Quality Assurance and Quality Control

Quality assurance is a required element of all USEPA-
sponsored studies that involve the collection and analysis
of environmental samples (U.S. Environmental Protection
Agency, 2003). This meant that all participants of the field
teams received in-depth training on methods and procedures
from USEPA or from experienced USGS personnel that had
successfully completed the training and had previously served
as field crew members. All field crew members also were Figure 13. Crew members calibrated water-quality instruments
provided with copies of the EMAP-West field manual and prior to collecting field measurements.
Calibration standards were purchased from the USGS The middle site on each stream was selected by USEPA
Quality of Water Service Unit in Ocala, Florida, or from the as an assessment site for EMAP-West. Data-collection
National Water Quality Laboratory in Denver, Colorado. activities at these two sites (table2, sites3 and6) included
Prior to calibration, an aliquot of stream water was analyzed, assessments of physical, chemical, and biological condi-
and then calibration standards were selected that bracketed tions. Samples for the analysis of water chemistry and benthic
the expected value for the stream water. The instrument was macroinvertebrate assemblages were collected by the USGS at
then calibrated using the appropriate standard(s). Only valid these two sites and sent to USEPA for analysis. Data-collec-
standards were used for instrument calibration; standards that tion activities at the other four stream assessment sites (table2,
exceeded expiration dates were discarded. Standards for pH sites1, 4, 5, and 8) included similar assessments of physical
and specific conductance were immersed in the stream for habitat and vertebrate identification and enumeration; how-
about 20minutes prior to instrument calibration so that the ever, only field properties were measured to determine basic
temperature of the stream and the standards were similar. water quality, and no samples were submitted to the USEPA
Generally, two-point calibrations were used for pH and for the analysis of water chemistry.
specific conductance. Measurements generally were recorded
on field sheets when the instrument stabilized and when two
consecutive readings varied by less than 0.3milligram per
liter for dissolved oxygen, 0.1 pH unit, 5percent for specific Geologic Influences on Stream
conductance, and 0.2C for water temperature. Condition
This section describes the results of assessments con-
Chemical Analysis ducted on two streams in south-central South DakotaBear-
The chemical analysis of stream water samples was in-the-Lodge and Black Pipe Creeks. These assessments were
completed by the USEPA or their contract laboratories. A list conducted in order to demonstrate the geologic influences on
of associated data reporting criteria and methods used for the stream conditions. Basin characteristics, streamflow, water
chemical analysis of water samples are presented in tables4 quality, vertebrate richness, and physical habitat are described.
and5, respectively, in the Supplemental Information section
(U.S. Environmental Protection Agency, written commun.,
2005). That communication also summarizes the methods for
Basin Characteristics and Streamflow
the collection, handling, processing, analysis, and manage- The drainage basins for Bear-in-the-Lodge Creek
ment of EMAP data. includes portions of the Western High Plains and the Northern
Great Plains ecoregions, while the drainage basin for Black
Methods for Characterizing Geologic Influences Pipe Creek lies entirely within the Northern Great Plains
ecoregion (fig.2). A series of benches and buttes, underlain
on Stream Condition by Tertiary sandstones, siltstones, and shale is present in the
southern portion of the study area (Malo, 1997). Silts and
Geology can have a substantial influence on the natural
conditions of a stream and further complicates the evaluation clays of the White River Group of Tertiary-age (Oligocene
and Eocene) are present in the northern part of the study area
of human influences on stream condition. One obvious exam-
(fig.3).
ple of this occurs when streams transition from mountainous
The drainage basin of Bear-in-the-Lodge Creek encom-
reaches with steep gradients to plains reaches with lesser gra-
passes approximately 365mi2. The elevation at the assess-
dients. More subtle changes can occur in other settings as well.
ment site on upper Bear-in-the-Lodge (site1) is about 2,570ft
A series of field surveys, incorporating many of the methods
previously described for conducting stream assessments for above NGVD29, and the elevation at the lower site (site4) is
about 2,280ft above NGVD29. The drainage basins of both
the EMAP-West, were conducted at several predetermined
streams are entirely within a single hydrologic unit (fig.3) as
points along the longitudinal profile of two streamsBear-in-
designated by the hydrologic unit map for the State of South
the-Lodge and Black Pipe Creeksin order to demonstrate
Dakota (U.S. Geological Survey, 1978). The headwaters of
the geologic influences on stream condition.
Bear-in-the-Lodge Creek are located in northwestern Ben-
Physical habitat and vertebrate data were collected at
nett County in an area where intermittent eolian deposits and
three sites along the longitudinal profiles of Bear-in-the-
remnants of the Pliocene-age Ogallala Formation overlie
Lodge Creek and Black Pipe Creek (fig.3) during a one-time
the Miocene-age Arikaree Formation (fig.3). The Ogallala
assessment in 2004, in order to document differences between
Formation is a fine- to medium-grained sandstone containing
upstream sites and downstream sites with respect to in-stream
some silty clay; the Arikaree Formation is an interbedded cal-
and near-stream conditions. Along with physical habitat and
careous sand, silt, and clay (Ellis and Adolphson, 1971). The
vertebrate data, water chemistry data were collected only at
stream flows to the southeast and then abruptly turns north
the middle site on each stream. Site number and site type are
and flows northwest through Jackson County where it crosses
provided in table2.
Geologic Influences on Stream Condition 23
Table 2. Information for sites used to characterize geologic influences.

[USGS, U.S. Geological Survey; USEPA, U.S. Environmental Protection Agency; EMAP, Environmental Monitoring and Assessment Program]
Site number
(fig.3) USGS station number Site name Site type
1 433151101480700 Upper Bear-in-the-Lodge Creek USGS stream assessment site
2 06446700 Bear-in-the-Lodge Creek near Wanblee, SD USGS streamflow gaging station (not a stream
assessment site)
3 433338101482100 Bear-in-the-Lodge Creek USEPA/EMAP reference site
4 434027101502600 Lower Bear-in-the-Lodge Creek USGS stream assessment site
5 432735101100300 Upper Black Pipe Creek USGS stream assessment site
6 433822101125500 Black Pipe Creek USEPA/EMAP reference site
7 06447230 Black Pipe Creek near Belvidere, SD USGS streamflow gaging station (not a stream
assessment site)
8 434633101134000 Lower Black Pipe Creek USGS stream assessment site
the White River Group just prior to joining the White River. average annual air temperature for the period 19712000 is
The White River Group is a poorly consolidated siltstone and about 47.3F, with an average of 72.8F for July and an aver-
claystone containing some beds of fine-grained sand (Ellis and age of 22.0F for January.
Adolphson, 1971). Much of western South Dakota has been in a persistent
The drainage basin of Black Pipe Creek encompasses drought since the latter part of the 1990s. Hydrologic condi-
approximately 250mi2. Elevations range from about 2,530ft tions for water year 2004 (October1, 2003, through Septem-
above NGVD29 (site5) at upper Black Pipe Creek to about ber30, 2004) were much different than the wetter conditions
2,020ft above NGVD29 at the lower site (site8). The head- experienced during the mid- to early 1990s, and generally
waters of Black Pipe Creek are located in northeast Bennett resulted in precipitation and streamflow levels that were well
County, in an area where intermittent eolian deposits over- below normal throughout much of western South Dakota. The
lie the Arikaree Formation. Some remnants of the Ogallala 2004 U.S. drought monitor map (National Oceanographic and
Formation also are present in the area. The stream flows to Atmospheric Administration, 2004) showed that the lower
the northeast into Mellette County where it flows across the one-third of South Dakota, which includes the study area, was
outcrop of the White River Group. The stream turns north and under severe to extreme drought conditions at the time the
then makes contact with isolated outcrops of terrace deposits stream assessments were conducted during June 2004. As a
of Quaternary age. The stream turns and flows to the north- result, most perennial streams probably experienced reduced
west across outcrops of the Late Cretaceous-age Pierre Shale. streamflow due to extended period of intense drought condi-
The Pierre Shale is a dark gray marine shale and mudstone tions.
containing some layers of bentonite (Ellis and Adolphson, The USGS has operated streamflow gaging stations on
1971). The stream then flows across various isolated outcrops Bear-in-the-Lodge and Black Pipe Creeks (fig.3) for several
consisting of alluvium or eolian deposits just prior to joining years. Streamflow data have been collected at continuous gag-
the White River near the Jackson and Mellette County line. ing station 06446700, Bear-in-the-Lodge Creek near Wanblee,
The climate, which is characteristic of the northern Great SD (table2, site2), for water years 1995 through 2003 and are
Plains, is semi-arid with cold winters and hot summers. The presented graphically in figure14. Streamflow data also have
following climate data was obtained from the South Dakota been collected at continuous gaging station 06447230, Black
State University (2005). Most of the precipitation falls during Pipe Creek near Belvidere, SD (table2, site7), from 1993 to
the growing season between April and September. Climato- 2003 and are presented graphically in figure15. The annual
logical data available for Martin, South Dakota (located about mean streamflow is 24.3ft3/s at site2 and 32.1ft3/s at site7
20 miles south of the study area), for the period 19712000 (Burr and others, 2004).
indicate that May is typically the wettest month with an aver- Stream assessment sites on Bear-in-the-Lodge Creek
age of 3.36in. of precipitation, and December typically is the were visited during June1516, 2004, and at that time,
driest month with an average of 0.3in. of precipitation. The streamflow at the upper site (site1 in fig.3) measured
6.83ft3/s. Streamflow at site3, the candidate reference site Lodge Creek had a slightly larger richness of vertebrate spe-
selected by USEPA, measured 7.13ft3/s, and streamflow cies than Black Pipe Creek. The total number of fish (exclud-
at site4 measured 5.92ft3/s. Streamflow data presented in ing crayfish) caught from all three reaches also was much
graphB of figure14 indicate that the monthly mean stream- higher at Bear-in-the-Lodge Creek (547) than at Black Pipe
flow for June at the streamflow gaging station (site2) for the Creek (147). More fish were found at the lower site (site4) on
period of record is about 50ft3/s. Measured streamflow at all Bear-in-the-Lodge Creek than at sites farther upstream. Prox-
three sites on Bear-in-the-Lodge Creek was less than the 10th imity of site4 to the confluence with the White River might
percentile of values recorded for June at site2 for the period of help to explain the high number of fish caught. Relatively
record. large fish ranging from 183mm at the upper site to 532mm at
Sites on Black Pipe Creek were visited during June89, the lower site were found in Bear-in-the-Lodge Creek.
2004, and at that time, streamflow at the upper site (site5 in Black Pipe Creek had slightly lower species richness
fig.3) measured 1.45ft3/s. Streamflow at site6, the candi- overall than Bear-in-the-Lodge Creek. A slightly larger rich-
date reference site selected by USEPA, measured 0.38ft3/s, ness of vertebrate species was found at the lower site (site8)
and streamflow at site8 was estimated visually as 0.01ft3/s. on Black Pipe Creek than at the two upstream sites. Proximity
Streamflow data presented in graph B of figure15 indicate of site8 to the confluence with the White River might help
that the monthly mean streamflow for June at site7 for the to explain the higher richness. Fish such as channel catfish
period of record is about 68ft3/s. The streamflow measure- (310mm) and river carpsucker (152mm) were found only at
ment for site5 fell between the 10th and 25th percentiles of the lower site. These fish are common to the main stem White
the June values; however, streamflow measurement for sites6 River (Fryda, 2001) and tended to be some of the larger fish
and8 were less than the 10th percentile of values recorded at caught in Black Pipe Creek. Examples of fish caught, identi-
the streamflow gaging station site on Black Pipe Creek during fied, and measured at Bear-in-the-Lodge Creek or Black Pipe
the period of record. Creek are shown in figure16.
Water Quality Physical Habitat

Full sets of samples for the characterization of stream- Physical habitat data collected from three reaches on
water chemistry were collected only at site3 on Bear-in-the- Bear-in-the-Lodge Creek (fig.17) and three reaches on Black
Lodge Creek and at site6 on Black Pipe Creek. These two Pipe Creek (fig.18) during June 2004 are provided in tables9
sites were selected by USEPA because they met their pre- and10, respectively, in the Supplemental Information section.
liminary candidate reference site screening criteria. Results In addition to the physical measurements and determinations,
of the water-quality analyses are provided in table6 in the rapid habitat assessments also were used to characterize the
Supplemental Information section. A summary of the analyti- habitat of both streams. Table11 contains the responses of the
cal methodologies used for determination of stream-water field crews to their visual assessment of stream habitat and
chemistry are provided in table5. Field measurements were the area immediately adjacent to the stream. The procedures
completed for all six sites and also are included in table6. used for the rapid habitat assessment follow those originally
Values for dissolved oxygen and specific conductance described by Barbour and others (1999).
generally increased from upstream to downstream locations on Substrate particle size for each site was characterized by
Bear-in-the-Lodge Creek. Values for pH and water tempera- averaging the 5-point pebble counts collected at 11 transects.
ture generally decreased from upstream to downstream loca- Similar measurements also were made at points midway
tions. Decreasing water temperatures could be an indication of between established transects so that data were collected from
ground-water inflows. 21 transects at a total of 105 points along the stream reach.
Values for dissolved oxygen, pH, and water temperature Average substrate particle size for each site was the mean
generally increased from upstream to downstream locations on of size class for the 105 total pebble counts. Upper Bear-in-
Black Pipe Creek. Most notably, values for specific conduc- the-Lodge Creek (site1, table2 and fig.17A) has an average
tance increased from 434microsiemens per centimeter at substrate composition generally consisting of coarse to fine
25degrees Celsius (S/cm) at site5 to 1,342S/cm at site8, gravels that gradually transitions to silt and clays at site3.
probably as a result of contact with the underlying Pierre The substrate largely is composed of hardpan and silt and clay
Shale. at site4. Thus, average substrate sizes decreased in a down-
stream direction.
Fish cover at the upper site largely is composed of
Vertebrate Richness overhanging vegetation and woody debris. The predominant
fish cover at site3 (fig.17B) is composed of woody debris
Vertebrate data collected from three reaches on Bear-
and macrophytes and then transitions to macrophytes at site4
in-the-Lodge Creek and three reaches on Black Pipe Creek
(fig.17C).
during June 2004 are provided in tables7 and8, respectively,
in the Supplemental Information section. Overall, Bear-in-the-
A. Annual mean flow B. Distribution of monthly mean flow
100 1,000
100
10 10
Maximum
90th percentile
1 75th percentile
FLOW, IN CUBIC FEET PER SECOND

Mean
50th percentile
STREAMFLOW, IN CUBIC FEET PER SECOND

25th percentile
10th percentile
Minimum
1 0.1
1995 1996 1997 1998 1999 2000 2001 2002 2003 OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP
C. Duration curve of daily mean flow D. Duration hydrographs of daily mean flow
1,000 1,000
100 100
10 10
Flow, in
Percent cubic feet
of time per second
95 2.6
90 4.3
1 75 7.5 1
50 13.0 Maximum
DISCHARGE, IN CUBIC FEET PER SECOND

25 23.0 75 percent
10 40.0 50 percent
5 66.0 25 percent
Minimum
0.1 0.1
0.1 1 2 5 10 20 30 40 50 60 70 80 90 95 98 99 99.9 OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP
PERCENT OF TIME INDICATED VALUE WAS EQUALED OR EXCEEDED
Figure 14. Variations in annual, monthly, and daily mean streamflow for station 06446700, Bear-in-the-Lodge Creek near Wanblee, SD, water years 19952003.
A. Annual mean flow B. Distribution of monthly mean flow
1,000 1,000
100
100
10
1
10
Maximum

90th percentile
0.1 75th percentile
Mean
STREAMFLOW, IN CUBIC FEET PER SECOND

50th percentile
25th percentile
10th percentile
Minimum
1 0.01
1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP
C. Duration curve of daily mean flow D. Duration hydrographs of daily mean flow
10,000 10,000
1,000 1,000
100 100
10 10
Flow, in
Percent cubic feet
of time per second
1 1
95 0.31
90 0.80
75 2.7
Maximum
50 8.4 75 percent
DISCHARGE, IN CUBIC FEET PER SECOND

0.1 25 23.0 0.1 50 percent
10 87.0 25 percent
5 199.0 Minimum
0.01 0.01
0.1 1 2 5 10 20 30 40 50 60 70 80 90 95 98 99 99.9 OCT NOV DEC JAN FEB MAR APR MAY JUN JUL AUG SEP
PERCENT OF TIME INDICATED VALUE WAS EQUALED OR EXCEEDED
Figure 15. Variations in annual, monthly, and daily mean streamflow for station 06447230, Black Pipe Creek near Belvidere, SD, water years 19932003.
A B
Figure 16. Examples of fish caught, identified, and measured at Bear-in-the-Lodge or Black Pipe Creeks include (A) channel
catfish and (B) river carp sucker.
Riparian cover consisted of sparse to moderate densities Rapid habitat assessments for Bear-in-the-Lodge Creek
of big and small trees and grasses at the upper site on Bear-in- tended (table11) to rate this stream between optimal and
the-Lodge Creek. The predominate riparian cover transitioned sub-optimal for most categories. Bank stability and vegetative
to grasses at site3 and was largely composed of barren dirt at protection tended to decline somewhat at the middle and lower
the lower site (table9). sites.
Thalweg depths and wetted widths varied among sites on Upper Black Pipe Creek (site5) generally had a sub-
Bear-in-the-Lodge Creek and showed no trend in relation to strate composition of silt and sand. Substrate composition was
stream size. The average maximum thalweg depth for all tran- largely silt and clay at the middle site (site6), and consisted
sects at the upper site (site1) was 42.8cm. The largest maxi- of sand and fine gravel at the lower site (site8). Thus, average
mum thalweg depth measurement at this site was 62cm at substrate size increased from silt to fine gravel in a down-
transect J, and the smallest maximum thalweg depth measure- stream direction (table10).
ment at this site was 23cm at transect H. The average wetted Fish cover at site5 on Black Pipe Creek primarily was
width of the reach was 3.9m, with a minimum width of 2.6m composed of overhanging vegetation and filamentous algae
at transect D and a maximum width of 5.3m at transect I. (fig.18A). Overhanging vegetation was the predominant fish
The average maximum thalweg depth for all transects at cover at site6 (fig.18B), whereas macrophytes provided the
the middle site (site3) was 79.7cm. The largest maximum dominant fish cover at site8 (fig.18C). Fish cover was largely
thalweg depth measurement at this site was 120cm at tran- categorized as sparse throughout the three reaches on Black
sectI, and the smallest maximum thalweg depth measurement Pipe Creek.
at this site was 38cm at transect J. The average wetted width Riparian cover at the upper and middle sites on Black
of site3 was 4.0m, with a minimum width of 2.9m at transect Pipe Creek was a mixture of grasses and woody shrubs. Ripar-
H and a maximum width of 5.5m at transect I. ian cover was largely absent at the lower site and consisted of
The average maximum thalweg depth for all transects grasses and bare dirt.
at the lower site (site4) was 51.4cm. The largest maximum The average maximum thalweg depth for all transects at
thalweg depth measurement recorded at this site was 90cm at upper Black Pipe Creek (site5) was 30.8cm. The largest max-
transect I, and the smallest maximum thalweg depth measure- imum thalweg depth measurement at this site was 41cm at
ment at this site was 30cm at transects A, B, and C. The transect I, and the smallest maximum thalweg depth measure-
average wetted width of site4 was 5.7m, with a minimum ment at this site was 22cm at transect D. The average wetted
width of 4.4m at transect C and a maximum width of 7.2m at width of the reach was 2.4m, with a minimum width of 1.6m
transect J. at transect A and a maximum width of 3.9m at transect F.
The stream channel was characterized as largely consist- The average maximum thalweg depth for all transects
ing of riffles at site1, and transitioned into a glide throughout at the middle site on Black Pipe Creek (site6) was 54.8cm.
most of the transects at site3. Site4 was characterized as The largest maximum thalweg depth measurement at this site
either a glide or glide/riffle combination throughout the reach. was 87cm at transect E, and the smallest maximum thalweg
A A
B
B
Figure 18. Upper Black Pipe Creek, assessment sites:

(A) upper site (site 5), (B) middle site (site 6), and (C) lower
site (site 8).
Figure 17. Bear-in-the-Lodge Creek, assessment sites:

(A) upper site (site 1), (B) middle site (site 3), and (C) lower
site (site 4).
Summary 29
depth measurement at this site was 16cm at transect J. The of the ecological condition of surface waters across a large
average wetted width of the reach was 2.0m, with a minimum geographic area of the West; and (2)demonstrate the effective-
width of 1.2m at transect J and a maximum width of 2.8m at ness of those tools in a large-scale assessment.
transectC. The resource population of interest for EMAP-West was
The average maximum thalweg depth for all transects at all perennial streams and rivers represented in USEPAs River
lower Black Pipe Creek (site8) was 14.1cm. The largest max- Reach File (RF3), with the exception of the lower portions of
imum thalweg depth measurement at this site was 26cm at the Great Rivers (the Columbia, Snake, Colorado, and Mis-
transect D, and the smallest maximum thalweg depth measure- souri Rivers). Assessments sites were selected randomly using
ment at this site was 6cm at transect G. The average wetted a probability design where each site had a known probability
width of the reach was 2.2m, with a minimum width of 0.7m for selection.
at transect H and a maximum width of 4.2m at transect A. This was done to ensure that all types of streams are
The stream channel at site5 on upper Black Pipe Creek included in the final list of sites and to allow for adequate
was categorized as a glide that transitioned into a glide/riffle spacial representation.
throughout the reach at site6. The stream channel at the lower During 2000, USEPA completed assessments at 22ran-
site (site8) consisted largely of a series of interconnected domly selected wadeable stream sites in South Dakota. In
pools throughout the reach. 2001, the South Dakota Department of Game, Fish and Parks
No rapid habitat assessment rating was completed for (GF&P) and the U.S. Geological Survey (USGS) entered into
upper Black Pipe Creek (site 5, table11 in the Supplemental a cooperative agreement to complete the remaining stream
Information section). Sites 6 and 8 generally received ratings assessments in South Dakota for the duration of the EMAP-
that ranged from suboptimal to poor for most categories that West study. During 20012003, USGS and GF&P completed
evaluated in-stream and near-stream conditions. another 42 stream assessments bringing the total number of
randomly selected stream assessments to 64. USGS personnel
used several monitoring techniques developed by the USEPA
Vertebrate /Physical Habitat Associations for conducting the ecological assessments. Many chemical,
physical, and biological indicators were assessed at selected
Differences in thalweg depth and wetted width between
sites that included water chemistry, physical habitat, periphy-
Bear-in-the-Lodge and Black Pipe Creeks may explain pat-
ton assemblages, benthic macroinvertebrate assemblages,
terns in vertebrate diversity and abundance. On average, Bear-
aquatic vertebrate communities, and fish tissue contaminants.
in-the-Lodge Creek had a deeper thalweg and wider wetted
EMAP-West was expanded beginning in 2002 to include
width than Black Pipe Creek. Therefore, habitat volume for
the selection and sampling of candidate reference sites
aquatic vertebrates (that is, fish) was greater in Bear-in-the-
throughout South Dakota. Candidate reference sites were not
Lodge Creek than Black Pipe Creek. A longitudinal thalweg
selected randomly but were specifically selected because it
profile was plotted in relation to transect location for each site.
was generally believed that they possessed the best attain-
Because vertebrate location to nearest transect was recorded
able aquatic conditions within the major LevelIII Ecoregions
during sampling, vertebrate location to thalweg depth could
present in South Dakota. Inclusion of candidate reference sites
be determined. Accordingly, most vertebrates were collected
into EMAP-West provided a valuable mechanism for assess-
nearest transects that represented the deepest pools in the sam-
ing the overall health of sites randomly selected by USEPA
ple reach for all sites. Given the intermittent nature of streams
throughout the State by providing standards or benchmarks
in the White River drainage basin, pools provide critical ref-
that could be compared against existing aquatic conditions at
uge for fish during low-flow periods. The continuing drought
randomly selected sites. Guidelines for selecting candidate
during this study period likely strengthened the importance of
reference sites were developed jointly by several State and
pool habitat for fish. The greater availability of pool habitat,
Federal agencies to ensure that sites were representative of a
and thus refuge area, in Bear-in-the-Lodge Creek would allow
variety of hydrogeological, ecological, and land-use settings
this stream to support a greater diversity and abundance of fish
found throughout South Dakota. During 20022004, USGS
than Black Pipe Creek.
and GF&P completed stream assessments for 45 candidate
reference sites. Thus, for the 5-year duration of EMAP-West
(20002004), assessments were completed at 109 sites.
Summary Eighteen repeat assessments were completed at 12 of the 64
randomly selected assessment sites to provide estimates of
During 2000, the U.S. Environmental Protection Agency important components of variability and for quality-assurance
(USEPA) initiated a 5-year study called the Environmental purposes. Repeat assessments were not included in the 109site
Monitoring and Assessment Program-West (EMAP-West). assessment total.
The two primary objectives of the surface-water component This report provides an overview of EMAP-West activi-
of the EMAP-West were to (1)develop the monitoring tools ties in South Dakota during 20002004. It presents stream
(biological indicators, stream survey design, and estimates of assessment site locations and describes the methods used to
reference condition) necessary to produce unbiased estimates collect the chemical, physical, and biological data that will be
used by USEPA to estimate the ecological conditions of our in the lower reaches. Rapid habitat assessments metrics gener-
Nations stream and river resources in the 12 western States ally were scored as good except for sediment deposition and
included in EMAP-West. riffle frequency.
Relatively early in the EMAP-West stream-assessment Average substrate size for Black Pipe Creek increased
process, it became apparent that for some streams in south- from silt to fine gravel in a downstream direction. In-stream
central South Dakota, in-stream conditions varied consid- fish cover was composed of overhanging vegetation and algae
erably over relatively short distances of only a few miles. in the upper reaches and transitioned to macrophytes in the
These changes appeared to be a result of geomorphic changes lower reaches. However, fish cover was sparse throughout
associated with changes in the underlying geology. For these all reaches. Riparian cover largely consisted of grasses and
streams, moving stream assessment sites short distances woody shrubs in the upper reaches of Black Pipe Creek and
upstream or downstream had the potential to provide substan- transitioned to grasses and bare dirt in the lower reaches. The
tially different bioassessment data. In order to obtain a better stream channel was largely a glide in the upper reaches and
understanding of how geology influences stream conditions, transitioned to a glide/riffle in the middle reaches and to a
two streams located in south-central South Dakota were series of interconnected pools in the lower reach. No rapid
chosen for multiple stream sampling at sites located along habitat assessments were completed for the upper reach, but
their longitudinal profile at points where notable changes in the lower reaches were categorized as poor for most in-stream
geomorphology were observed. Subsequently, three sites on and near-stream conditions.
Bear-in-the-Lodge Creek and three sites on Black Pipe Creek
were selected for multiple stream sampling using EMAP-West
protocols so that more could be learned about the geologic
influences on stream conditions. References
Values for dissolved oxygen and specific conductance
generally increased from upstream to downstream locations American Public Health Association, 1989, Standard methods
on Bear-in-the-Lodge Creek. Values for pH and water tem- for the examination of water and wastewater (17th ed.):
perature generally decreased from upstream to downstream Washington, D.C., American Public Health Association.
locations. Decreasing water temperature could be indicative of
Barbour, M.T., Gerritsen, J., Snyder, B.D., and Stribling, J.B.,
ground-water inflows.
1999, Rapid bioassessment protocols for use in streams and
Values for dissolved oxygen, pH, and water temperature
wadeable riversperiphyton, benthic macroinvertebrates,
generally increased from upstream to downstream locations
and fish (2d ed.): Washington, D.C., U.S. Environmental
on Black Pipe Creek. The increase in temperature at the lower
Protection Agency, Office of Water, EPA 841B99002,
sites is a result of less dense riparian cover, and the warmer
accessed on December5, 2005, at http://www.epa.gov/
water also could account for the lower concentrations of dis-
owow/monitoring/rbp/].
solved oxygen found in the lower reaches of Black Pipe Creek.
Values for specific conductance were more than three times Burr, M.J., Teller, R.W., Neitzert, K.M., 2004, Water resources
greater at the lower site (1,342microsiemens per centimeter data, South Dakota, water year 2003: U.S. Geological Sur-
(S/cm)) than at the upper site (434S/cm). The increase vey Water-Data Report SD031, 491p.
probably occurs when the stream transitions from contacting
the underlying Arikaree Formation to contacting the underly- Ellis, M.J., and Adolphson, D.G., 1971, Hydrology of the
ing Pierre Shale. Pine Ridge Indian Reservation, South Dakota: U.S. Geo-
Vertebrate richness was found to be slightly higher for logical Survey Hydrologic Investigations Atlas HA357,
Bear-in-the-Lodge Creek (547 total number of fish) than for scale1:125,000.
Black Pipe Creek (147 total number of fish). On average,
Fenneman, N.M., 1946, Physical divisions of the United
reaches on Bear-in-the-Lodge Creek had a deeper thalweg
States: U.S. Geological Survey map prepared in coopera-
and wider wetted stream width than Black Pipe Creek. This
tion with the Physiographic Commission, U.S. Geological
resulted in a larger habitat volume of aquatic vertebrates in
Survey, scale 1:700,000 (reprinted 1964).
Bear-in-the-Lodge Creek than in Black Pipe Creek and prob-
ably is the reason for the higher vertebrate richness found in Fore, L.S., Karr, J.R., and Wisseman, R.W., 1996, Assess-
Bear-in-the-Lodge Creek. ing invertebrate responses to human activities, evaluating
Average substrate size decreased in a downstream direc- alternative approaches: Journal of the North American
tion for Bear-in-the-Lodge Creek. In-stream fish cover also Benthological Society, v.15, p.212231.
transitioned from woody debris to macrophytes in a down-
stream direction for Bear-in-the-Lodge Creek, whereas the Fryda, D.D., 2001, A survey of the fishes and habitat of the
predominate riparian cover transitioned from trees to barren White River, South Dakota: Brookings, South Dakota State
dirt in the lower reaches. The stream channel for Bear-in-the- University, unpublished M.S. thesis, 100p.
Lodge Creek largely consisted of riffles in the upper stream
reaches and transitioned into glide or glide/riffle combinations
References31
Klemm, D.J., Lewis, P.A., Faulk, F., and Lazorchak, J.M., South Dakota State University, 2005, South Dakota climate
1990, Macroinvertebrate field and laboratory methods for and weather: accessed June6, 2005, at http://climate.
evaluating the biological integrity of surface waters: Cincin- sdstate.edu/climate_site/site_map.htm#
nati, U.S. Environmental Protection Agency, Environmental
Monitoring Systems Laboratory, EPA/600/490/030. Stanley, D.L., 1996, New standard operating procedures and
quality-control practices for the U.S. Geological Survey
Larsen, D.P., 1997, Sample survey design issues for bioassess- National Field Quality Assurance Program since January
ment of inland aquatic ecosystems: Human and Ecological 1994: U.S. Geological Survey Open-File Report 96130,
Risk Assessment, v.3, p.979991. 88p.
Larsen, D.P., Kincaid, T.M., Jacobs, E.E., and Urquhart, N.S., Stevens, D.L., Jr., and Olsen, A.R., 2004, Spatially balanced
2001, Designs for evaluating local and regional trends: sampling of natural resources: Journal of American Statisti-
Bioscience, v.51, p.10691078. cal Association, v.99, no.465, p.262278.
Malo, D., 1997, South Dakotas physiographic regions: Suter, G.W., 1993, Ecological risk assessment: Boca Raton,
Brookings, Plant Science Department, South Dakota State Fla., CRC Press, LLC Publishers, 538p.
University, accessed June11, 2005, at http://www.northern.
edu/natsource/EARTH/Physio1.htm U.S. Environmental Protection Agency, 1987a, Future
Riskresearch strategies for the 1990s: Washington, D.C.,
Martin, J.E., Sawyer, F.J., Fahrenbach, M,D., Tomhave, U.S. Environmental Protection Agency Science Advisory
D.W., and Schulz, L.D., 2004, Geologic map of South Board SABEC88040.
Dakota: South Dakota Geological Survey, General Map 10,
scale1:500,000. U.S. Environmental Protection Agency, 1987b, Handbook
of methods for acid deposition studieslaboratory analy-
National Oceanographic and Atmospheric Administration, ses for surface water chemistry: Washington, D.C., U.S.
2004, The U.S. drought monitor: accessed June2, 2005, at Environmental Protection Agency, Office of Research and
http://drought.unl.edu/dm/archive/2004/drmon0615.htm Development, EPA/600/487/026.
Omernik, J.M., 1987, Ecoregions of the conterminous U.S. Environmental Protection Agency, 1997, Environmental
United States (map supplement): Annals of the Associa- Monitoring and Assessment Programintegrated quality
tion of American Geographers, v.77, no.1, p.118125, assurance project plan for surface waters research activi-
scale1:7,500,000. ties: Corvallis, Oregon, National Health and Environmental
Effects Research Laboratory, Western Ecology Division.
Peck, D.V., Lazorchak, J.M., and Klemm, D.J., eds., 2003,
Environmental Monitoring and Assessment Programsur- U.S. Environmental Protection Agency, 1998, Environmental
face waters pilot studywestern pilot study field operations Monitoring and Assessment Program (EMAP): Washington,
manual for wadeable streams: Washington, D.C., U.S. Envi- D.C., Research Plan 1997, EPA/620/R98/002.
ronmental Protection Agency, accessed December2, 2005,
at http://www.epa.gov/wed/pages/projects/WADEABLE_ U.S. Environmental Protection Agency, 2000, Mid-Atlantic
MANUAL_APR_2003.pdf Highlands Streams Assessment: EPA-903-R-00-015, 64p.
Rantz, S.E., and others, 1982, Measurement and computation U.S. Environmental Protection Agency, 2001, Environmental
of streamflowVolume 1, Measurement of stage and dis- Monitoring and Assessment Programsurface waters
charge: U.S. Geological Survey Water-Supply Paper 2175, western pilot study field operations manual for wadable
284p. streams: accessed February14, 2005, at www.epa.gov/emap/
html/pubs/docs/groupdocs/surfwatr/field/fomws.html
Reynolds, Lou, Herlihy, A.T., Kaufmann, P.R., Gregory, S.V.,
and Hughes, R.M., 2003, Electrofishing effort required for U.S. Environmental Protection Agency, 2002, Biological
assessing species richness and biotic integrity in western assessments and criteriacrucial components of water
Oregon streams: North American Journal of Fisheries Man- quality programs: U.S. Environmental Protection Agency
agement, v.23, p.450461. Fact Sheet 822F02006, 6p.
Rosenberg, D.M., and Resh, V.H., 2001, Freshwater biomoni- U.S. Environmental Protection Agency, 2003, Overview of
toring and benthic macroinvertebrates: Norwell, Mass., the EPA quality system for environmental data and tech-
Kluwer Academic Publishers, 488p. nology: Washington, D.C., EPA/240/R02/00, accessed
December5, 2005, at http://www.epa.gov/quality1/qs-docs/
South Dakota Department of Environment and Natural overview-final/pdf
Resources, 2004, South Dakota integrated report for surface
water quality assessment: accessed June14, 2005, at U.S. Geological Survey, 1978, Hydrologic unit map State of
http://www.state.sd.us/denr/denr.html South Dakota: 1sheet, scale 1:500,000.
U.S. Geological Survey, 19972004, National field manual for

the collection of water-quality data: U.S. Geological Survey
Techniques of Water-Resources Investigations, book9,
chaps.A1A9, 2v., variously paged. [Available online at
http://pubs.water.usgs.gov/twri9A]. Chapters were origi-
nally published from 19971999; updates and revisions are
ongoing and are summarized at http://water.usgs.gov/owq/
FieldManual/mastererrata.html.
Supplemental Information
Table 3. General guidelines for consideration in selection of candidate reference sites.
1. General flow characteristicsTwo specific criteria: (A) Sufficiently perennial to maintain viable aquatic communities during most years;
and (B) can be waded in all but deepest of holes. Also a general guideline that tributaries near confluence with larger stream may make
ideal candidates.
2. Geographic distribution and representative characteristicsReference sites need to have a wide geographic distribution within the
State and represent the best attainable aquatic conditions within the designated area. In addition to having good representation for the four
major Omernik level III ecoregions (Omernik, 1987) within the State, a variety of different hydrogeologic/land-use/landscape settings need
to be addressed. Target areas might include:
Black Hills
Badlands (parts of White River and some of its tributaries)
Sand Hills (Little White/Keya Paha Rivers)
Western South Dakota shales (Cheyenne/Bad Rivers)
Western South Dakota sandstones/siltstones (Grand/Moreau Rivers)
Missouri River breaks
Upper James River
Lower James/Lower Big Sioux/Vermillion Rivers
Coteau des Prairies
Upper Big Sioux River

3. Consideration of core factors listed in U.S. Environmental Protection Agency Region 7 documentThe 11 core factors listed should
be an excellent starting point for evaluating candidate siteswastewater treatment plants (and other point sources of pollution), combined
animal feeding operations (CAFOs), instream habitat, raparian habitat, land use/land cover (broad scale), land use/land cover (site specific),
physical and chemical properties, altered hydrologic regime, biological metrics, faunal assemblages, and representativeness.
4. Geographic information system (GIS) analysis using selected coverages (land use, conservation easements, CAFOs, wastewater
discharges, and others)Again, no specific approach envisioned; however, numerous insights probably can be obtained by consideration
of available GIS coverages.
5. Long-term viability/security/accessibilityLong-term potential for maintenance in a minimal-influence condition would be beneficial.

Best prospects might include public ownership and permanent conservation easements, which also could be conducive to future site acces-
sibility. Physical accessibility of sites also could be a consideration.
6. Parallelism with other programsAnother desirable quality would be parallelism with other environmental programs such as various
Nataural Resource Conservation Service programs, availability of long-term water-quality data (305B monitoring sites, U.S. Geological
Survey or Tribal data), and biological data from previous surveys. Expressed interest from land-management agencies (see item 7) would
be beneficial.
7. Multiple recommendationsRecommendations from multiple sources (District Conservationists in overlapping areas, interested agen-
cies, collaborating agencies) would be indicative of high potential for candidate sites.
8. Professional judgmentIt is envisioned that no rigid method can be established to identify or score potential sites. Professional judgment
and discussions leading to consensus among collaborating agencies may be an important factor in finalizing selections.
Supplemental Information35
Table 4. Data reporting criteria for water chemistry analyses.

[From U.S. Environmental Protection Agency, written commun., 2005. mg/L, milligrams per liter; C, degrees Celsius;
eq/L, microequivalents per liter; S/cm, microsiemens per centimeter at 25 degrees Celsius; g/L, micrograms per liter;
NTU, nephelometric turbidity units; PCU, platinum cobalt units]
Number of Maximum number of

Measurement Units significant figures decimal places
Dissolved oxygen mg/L 2 1
Temperature C 2 1
pH pH units 3 2
Carbon, dissolved inorganic mg/L 3 2
Carbon, dissolved organic mg/L 3 1
Acid neutralizing capacity eq/L 3 1
Aluminum (total dissolved, total mono- eq/L 3 1

meric, and organic monomeric)
Specific conductance S/cm 3 1
Calcium, magnesium, sodium, and eq/L 3 2

potassium
Ammonium, chloride, nitrate, and eq/L 3 2

sulfate
Silica mg/L 3 2
Total phosphorus and total nitrogen g/L 3 2
Turbidity NTU 3 2
True color PCU 2 0
Total suspended solids mg/L 3 1

Table 5. Analytical methodologies for water chemistry.

[Quality-assurance classification: C, critical; N, non-critical. eq/L, microequivelents per liter; CO2, carbon dioxide; mg/L, milligrams per liter; S/cm, microsie-
mens per centimeter at 25 degrees Celsius; g/L, micrograms per liter; ppm, parts per million; UV, ultraviolet; PCU, platinum cobalt units; NTU, nephelometric
turbidity units; USEPA, U.S. Environmental Protection Agency; APHA, American Public Health Association; EDTA, ethylenediamine-tetraacetic acid]
Quality-
assurance
Property or classifica-
constituent tion Expected range Summary of method References
pH, closed system C 3 to 9 pH units Sample collected and analyzed without exposure USEPA 150.6 (modified);
to atmosphere; electrometric determination USEPA (1987)
(pH meter and glass combination electrode)
pH, equilibrated N 3 to 9 pH units Equilibration with 300 ppm CO2 for 1 hour prior USEPA 150.6 (modified);
to analysis; electrometric determination (pH USEPA (1987)
meter and glass combination electrode)
Acid neutralizing C -100 to 5,000 eq/L Acidimetric titration to pH 3.5, with modified USEPA 310.1 (modified);
capacity (ANC) Gran plot analysis USEPA (1987)
Carbon, dissolved N 0.1 to 50 mg C/L Sample collected and analyzed without exposure USEPA (1987)
inorganic (DIC)1 to atmosphere; acid-promoted oxidation to
CO2, with detection by infrared spectropho-
tometry
Carbon, dissolved C 0.1 to 30 mg C/L UV-promoted persulfate oxidation, detection by USEPA 415.2;
organic (DOC) infrared spectrophotometry USEPA (1987)
Conductivity C 1 to 500 S/cm Electrolytic (conductance cell and meter) USEPA 120.6;
USEPA (1987)
Aluminum, total dis- C 10 to 1,000 g/L Atomic absorption spectroscopy (graphite USEPA 202.2;
solved furnace) USEPA (1987)
Aluminum, mono- N 0 to 500 g/L Collection and analysis without exposure to APHA 3000-Al E.;
meric and organic atmosphere. Portion of sample passed through APHA (1989);
monomeric a cation exchange column before analysis to USEPA (1987)
obtain estimate of organic-bound fraction.
Colorimetric analysis (automated pyrocatechol
violet)
Major cations, dissolved

Calcium C 0.02 to 76 mg/L Atomic absorption spectroscopy (flame) USEPA 200.6;
(1 to 3,800 eq/L) USEPA (1987)
Magnesium C 0.01 to 25 mg/L

(1 to 2,000 eq/L)
Sodium C 0.01 to 75 mg/L

(0.4 to 3.3 eq/L)
Potassium C 0.01 to 10 mg/L

(0.3 to 250 eq/L)
Ammonium N 0.01 to 5 mg/L Colorimetric (automated phenate) USEPA 350.7;

(0.5 to 300 eq/L) USEPA (1987)
Table 5. Analytical methodologies for water chemistry.Continued
Quality-
assurance
Property or classifica-
constituent tion Expected range Summary of method References
Major anions, dissolved

Chloride C 0.03 to 100 mg/L Ion chromatography
(1 to 2,800 eq/L)
Sulfate C 0.05 to 25 mg/L

(1 to 500 eq/L)
Silica, dissolved N 0.05 to 15 mg/L Automated colorimetric (molybdate blue) USEPA 370.1 (modified);
USEPA (1987)
Phosphorus, total C 0 to 1,000 g/L Acid-persulfate digestion with automated colori- USGS I-4600-78;
metric determination (molybdate blue) Skougstad and others
(1979);
USEPA (1987)
Nitrogen, total N 0 to 25,000 g/L Alkaline persulfate digestion with determination USEPA 353.2 (modified);
of nitrate by cadmium reduction and deter- USEPA (1987)
mination of nitrite by automated colorimetry
(EDTA/sulfanilimide)
True color N 0 to 300 PCU Visual comparison to calibrated glass color disks USEPA 100.2 (modified);
APHA 204 A.;
USEPA (1987)
Turbidity N 1 to 100 NTU Nephelometric APHA 214 A.;

USEPA 180.1;
USEPA (1987)
Total Suspended N 1 to 200 mg/L Gravimetric USEPA 160.3;

Solids (TSS) APHA (1989)
For DIC, dissolved is defined as that portion passing through a 0.45-micron nominal pore-size filter. For other constituents, dissolved is defined as that
1
portion passing through a 0.4-micron pore-size filter (Nucleopore or equivalent).

Table 6. Water-quality data for sites on Bear-in-the-Lodge and Black Pipe Creeks.
[NTU, nephelometric turbidity units; mg/L, milligrams per liter; S/cm, microsiemens per centimeter at 25 degrees Celsius; deg. C, degrees Celsius; eq/L, microiequivelents per liter; ft3/s, cubic feet per sec-
ond; --, no data]
Specific
pH, whole, conduc- Temper- Magne- Potas-
Site Dissolved field tance, Temper- ature, Calcium, sium, sium, Sodium, ANC Chloride,
Site name number Date Turbidity oxygen (standard field ature, air water dissolved dissolved dissolved dissolved (eq/L as dissolved
(table 1) (fig. 3) sampled (NTU) (mg/L) units) (S/cm) (deg. C) (deg. C) (eq/L) (eq/L) (eq/L) (eq/L) CaCO3) (eq/L)
Upper Bear-in-the- 1 06-15-04 -- 9.3 7.7 503 24.0 22.1 -- -- -- -- -- --
Lodge Creek
Bear-in-the-Lodge 3 06-15-04 168 9.1 7.4 507 25.0 20.5 2,146.1 428.4 295.5 2,790.1 5,103.4 114
Creek
Lower Bear-in-the- 4 06-16-04 -- 10.3 7.6 519 17.0 17.7 -- -- -- -- -- --
Lodge Creek
Upper Black Pipe 5 06-08-04 -- 9.3 7.1 434 18.0 17.4 -- -- -- -- -- --

Creek
Black Pipe Creek 6 06-09-04 43.7 8.2 7.4 590 14.0 17.0 2,248.1 440.4 306.3 3,811.0 5,997.3 174.6
Lower Black Pipe 8 06-09-04 -- 9.6 7.6 1,342 17.0 18.7 -- -- -- -- -- --

Creek
Dis- Dis-
Ammo- Phos- Sele- solved solved Total sus-
Site Silica, Sulfate, nia, Nitrate, Nitrogen, phorous, nium, Zinc, organic inorganic Hydrox- Bicar- Car- pended Dis-
number dissolved dissolved dissolved dissolved total total dissolved dissolved Color carbon carbon ide bonate bonate solids charge
(fig. 3) (eq/L) (eq/L) (eq/L) (eq/L) (g/L) (eq/L) (eq/L) (eq/L) (PCU) (mg/L) (mg/L) (eq/L) (eq/L) (eq/L) (mg/L) (ft3/s)
1 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 6.83
3 44.9 417.4 2.5 15 1,223 444 0.1 0.0 20 5.34 56.1 2.4 4,574.8 105.3 344.8 7.13
4 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 5.92
5 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- 1.45
6 34.5 376.6 1.7 .0 872 147 .0 6.0 40 9.8 68.1 3.2 5,545.8 168.3 58.6 .383
8 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- .001
Table 7. Vertebrate information for Bear-in-the-Lodge Creek.

[--, no data]
Minimum length Maximum length

Date Species collected Tally (millimeters) (millimeters) Transect where found
Upper Bear-in-the-Lodge Creek (site 1 in fig.3)
061504 Flathead chub 26 69 143 A, B, C, D, E, I, J
Longnose Dace 1 52 -- I
Sand shiner 52 44 68 A, B, C, D, E G, I, J
Shorthead redhorse 5 163 175 A, C, D
Stonecat 4 121 183 D, E
Unknown crayfish 12 -- -- A, D, E, I, J
Bear-in-the-Lodge Creek (site 3 in fig.3)

061504 Channel catfish 15 57 255 E, I, J
Flathead chub 3 75 125 E
Green sunfish 1 53 -- E
Sand shiner 3 49 63 E, I, J
Shorthead redhorse 3 156 159 A, D, I
Stonecat 2 115 146 A, I
Unknown crayfish 1 -- -- F
Lower Bear-in-the-Lodge Creek (site 4 in fig.3)

061604 Black bullhead 4 52 130 F, G, I
Channel catfish 3 170 532 G, I
Flathead chub 114 57 127 A, B, C, D, E, F, G, H, I, J
Hybognathus spp 161 62 93 A, B, C, D, E, F, G, H, I, J
Sand shiner 103 50 62 A, B, C, D, E, F, G, H, I, J
Longnose dace 45 57 89 A, B, C, D, E, F, I, J
Red shiner 1 47 -- I
River carpsucker 1 241 -- I

Table 8. Vertebrate information for Black Pipe Creek.
[--, no data]
Minimum length Maximum length Transect where

Date Species collected Tally (millimeters) (millimeters) found
Upper Black Pipe Creek (site 5 in fig.3)
060804 Creek Chub 6 64 142 G, I, F, H
Long nose dace 5 55 84 F, H
Sand shiner 1 69 -- G
Unknown tapole 1 -- -- G
Black Pipe Creek (site 6 in fig.3)

060904 Flathead chub 13 78 115 A, C, E, G, F, H
Hybognathus spp 10 70 82 C, E, G, F
Lower Black Pipe Creek (site 8 in fig.3)

060904 Channel catfish 5 155 310 B
Flathead chub 38 62 100 B
Hybognathus spp 56 51 69 B
River carpsucker 4 144 152 B
Sand shiner 8 40 59 B
Table 9. Physical habitat data for sites on Bear-in-the-Lodge Creek.
[cm, centimeter; OV, overhanging vegetation; ST, small trees; G, grasses; BT, big trees; WD, woody dedris; NDC, no dominant cover; BD, barren dirt; M, marophytes; R, roots; WS, woody shrubs; --, no data]
Maxiumum
thalweg Wetted
Substrate Fish cover Riparian cover Riparian cover Human depth width Channel
Transect composition (dominant) left bank right bank influence (cm) (meters) type
Upper Bear-in-the-Lodge Creek (site 1 in fig.3)
A Silt/Clay Absent/Sparse Sparse/Moderate (ST,G) Sparse/Moderate (G) Pasture 50 3.6 Glide
(OV)
B Fine Gravel Absent/Sparse Sparse/Moderate (BT,G) Sparse/Moderate (ST,G) Pasture 35 3.4 Riffle
(OV)
C Coarse Gravel Absent/Sparse Sparse (NDC) Sparse (BD) Pasture 52 4.0 Riffle
(WD)
D Silt/Clay Absent/Sparse Sparse/Moderate (NDC) Sparse(G) Pasture 45 2.6 Riffle
(OV,WD,M)
E Fine/Coarse Absent/Sparse Sparse/Moderate (G) Sparse (BD) Pasture 38 4.1 Riffle
Gravel (OV,WD,M)
F Silt/Clay Sparse/Moderate Moderate (BD) Moderate (G,WS) Pasture 40 3.3 Rapid
(OV,WD,M)
G Coarse Gravel Absent/Sparse Sparse/Moderate (G,WS) Sparse/Moderate (G) Pasture 30 4.8 Riffle
(WD,R,OV)
H Coarse Gravel Absent/Sparse Sparse/Moderate (G,BD) Sparse (G) Pasture 23 4.5 Riffle
(OV)
I Fine Gravel Sparse/Moderate Sparse/Moderate (G,WS) Sparse/Moderate (G) Pasture 53 5.3 Glide
(OV,WD,M)
J Fine Gravel Absent/Sparse Sparse/Moderate (G) Sparse/Moderate (G) Pasture 62 4.0 Glide
(OV)
K Fine Gravel Sparse/Moderate Absent/Sparse Sparse/Moderate Pasture -- -- --
Bear-in-the-Lodge Creek (site 3 in fig.3)
A Silt/Clay Absent/Sparse Moderate (NDC) Moderate (NDC) Pasture 77 3.9 Glide
(NDC)
B Silt/Clay Moderate (WD,OV) Sparse (G) Sparse (G) Pasture 72 4.3 Glide
C Silt/Clay Sparse (NDC) Sparse/Moderate (G) Sparse/Moderate (G,BD) Pasture 94 4.2 Glide
D Silt/Clay Absent/Sparse (NDC) Sparse/Moderate (G) Sparse/Moderate (G) Pasture 67 3.7 Glide
E Silt/Clay Absent/Sparse Sparse/Moderate (G) Sparse/Moderate (G) Pasture 99 3.9 Glide
(WD,OV)
F Silt/Clay Sparse (M,OV) Sparse/Moderate (ST,G) Sparse/Moderate (G) Pasture 71 3.3 Glide
Supplemental Information 41
Table 9. Physical habitat data for sites on Bear-in-the-Lodge Creek.Continued
Maxiumum
thalweg Wetted
Substrate Fish cover Riparian cover Riparian cover Human depth width Channel
Transect composition (dominant) left bank right bank influence (cm) (meters) type
Bear-in-the-Lodge Creek (site 3 in fig.3)Continued
G Silt/Clay Sparse/Moderate Moderate (G) Sparse/Moderate (G) Pasture 75 3.6 Glide
(WD,OV)
H Silt/Clay Absent/Sparse Sparse/Moderate (NDC) Sparse/Moderate (G) Pasture 84 2.9 Glide
(NDC)
I Silt/Clay Absent/Sparse Sparse (G) Sparse (ST,G) Pasture 120 5.5 Glide
(M.WD,OV)
J Silt/Clay Absent/Sparse Moderate (NDC) Moderate (G) Pasture 38 4.5 Riffle
(OV)
K Silt/Clay Absent/Sparse Sparse Sparse Pasture -- -- --
Lower Bear-in-the-Lodge Creek (site 4 in fig.3)
A Sand/Coarse Absent (M,OV) Sparse (BD) Sparse (BD) Pasture 30 6.1 Riffle
Gravel
B Hardpan/Silt Absent/Sparse Moderate (NDC) Absent (BD) Pasture 30 5.5 Glide
(M,OV)
C Hardpan Absent (R,OV) Sparse (BD) Sparse (BD) Pasture 30 4.4 Glide
D Coarse Gravel Absent (OV) Absent/Sparse (BD) Absent/Sparse (BD) Pasture 36 4.9 Glide/Riffle
E Silt/Clay Absent (OV) Sparse (BD) Absent/Sparse (BD) Pasture 64 5.6 Glide/Riffle
F Hardpan/Silt Absent (NDC) Absent/Sparse (BD) Sparse (BD) Pasture 35 5.6 Glide
G Sand Absent (M,OV) Sparse (BD) Sparse (BD) Pasture 76 6.0 Glide
H Silt/Sand Absent (M,OV) Sparse (BD) Sparse/Moderate (BD) Pasture 63 6.2 Glide
I Silt/Clay Absent (OV) Absent/Sparse (G,BD) Absent/Sparse (G,BD) Pasture 90 5.7 Glide
J Silt/Clay Absent/Sparse (M,OV) Sparse/Moderate (G,BD) Sparse/Moderate (G,BD) Pasture 60 7.2 Glide/Riffle
K Silt/Sand Absent/Sparse Absent/Sparse Absent Sparse -- -- --
Table 10. Physical habitat data for sites on Black Pipe Creek.
[cm, centimeter; OV, overhanging vegetation; ST, small trees; G, grasses; BT, big trees; WD, woody dedris; NDC, no dominant cover; BD, barren dirt; M, macrophytes; R, roots; WS, woody shrubs; --, no data;
FA, filamentous algae]
Riparian cover Riparian cover Maxiumum

Substrate Fish cover left bank right bank Human thalweg Wetted width
Transect composition (dominant) (dominant) (dominant) influence depth (cm) (meters) Channel type
Upper Black Pipe Creek (site 5 in fig.3)
A Silt/Clay Sparse/Moderate (M,WD) Absent/Sparse (G) Absent/Sparse (G) Pasture 36 1.6 Riffle
B Fine Gravel Absent/Sparse (FA,WD) Sparse/Moderate (G) Sparse/Moderate (WS,G) Pasture 39 1.9 Riffle
C Sand Sparse (FA) Moderate (WS,G) Moderate (WS,G) Pasture 33 2.1 Glide
D Silt/Sand Sparse (NDC) Sparse (G) Sparse (G) Pasture 22 2.7 Glide
E Silt/Sand Sparse/Moderate Sparse/Moderate (G) Sparse (WS) Pasture 25 2.4 Glide
(FA,M,OV)
F Silt/Sand Sparse/Moderate Sparse (G) Sparse (G) Pasture 30 3.9 Glide
(FA,M,OV)
G Silt/Sand Sparse/Moderate (WD,OV) Sparse/Moderate (WS,G) Sparse/Moderate (WS,G) Pasture 35 2.1 Glide
H Silt/Sand Sparse (OV) Sparse/Moderate (WS) Absent (G) Trash/Pasture 23 2.5 Glide
I Sand Absent/Sparse (OV) Sparse (WS,G) Sparse (WS,G) Pasture 41 2.3 Glide
J Silt/Sand Sparse (OV) Sparse (G) Sparse (G) Trash/Pasture 24 2.1 Glide/Riffle
K Silt/Gravel Sparse Sparse/Moderate Sparse Trash/Pasture -- -- --
Black Pipe Creek (site 6 in fig.3)
A Silt/Clay Sparse (NDC) Sparse (G) Sparse (G) Pasture 47 2.0 Glide
B Silt/Clay Sparse (NDC) Sparse (G) Sparse (G) Pasture 66 2.4 Glide
C Silt/Clay Sparse (NDC) Sparse (G) Sparse (G) Pasture 50 2.8 Riffle
D Coarse Gravel Sparse/Moderate (WD,OV) Sparse/Moderate (WS,G) Sparse/Moderate (WS,G) Pasture 78 2.2 Glide/Riffle
E Silt/Clay Sparse (OV) Sparse/Moderate (WS,G) Sparse/Moderate (WS,G) Pasture 87 1.8 Glide
F Coarse Gravel Sparse (OV) Moderate/Heavy (WS,G) Sparse (G) Pasture 50 1.8 Glide/Riffle
G Silt/Clay Sparse/Moderate (WD,OV) Sparse (G,BD) Sparse (WS,G) Trash/Pasture 82 1.9 Glide
H Silt/Clay Sparse (OV) Sparse (G) Sparse (G) Pasture 36 2.0 Glide
I Sand/Silt Sparse (OV) Sparse (NDC) Sparse (NDC) Trash/Pasture 36 1.7 Riffle
J Fine Gravel Sparse (OV) Moderate (G,WS) Sparse (BD) Pasture 16 1.2 Glide
K Coarse Gravel Sparse Moderate Sparse Pasture -- -- --
Table 10. Physical habitat data for sites on Black Pipe Creek.Continued
Riparian cover Riparian cover Maxiumum

Substrate Fish cover left bank right bank Human thalweg Wetted width
Transect composition (dominant) (dominant) (dominant) influence depth (cm) (meters) Channel type
Lower Black Pipe Creek (site 8 in fig.3)
A Sand Sparse (M,OV) Absent/Sparse (G,BD) Absent (BD) Trash/Pasture/ 22 4.2 Pool
Riprap/
Bridge
B Sand Absent/Sparse (M,OV) Absent/Sparse (G,BD) Absent (BD) Trash/Pasture/ 15 2.1 Pool
Riprap/
Bridge
C Sand Absent/Sparse (M,OV) Absent/Sparse (G,BD) Absent (BD) Trash/Pasture/ 13 3.5 Pool
Riprap/
Bridge
D Fine Gravel Absent (OV) Sparse (G,BD) Absent (BD) Trash/Pasture/ 26 2.1 Pool
Riprap/
Bridge
E Hardpan/Sand Absent/Sparse (G) Absent/Sparse (G) Absent (BD) Trash/Pasture/ 20 2 Pool/Riffle
Riprap/
Bridge
F Sand Absent/Sparse (M,OV) Absent/Sparse (G,BD) Absent (BD) Trash/Pasture/ 7 2.2 Pool
Riprap/
Bridge
G Sand Absent/Sparse (M) Absent/Sparse (G,BD) Absent/Sparse (BD) Trash/Pasture/ 6 1 Pool
Riprap/
Bridge
H Fine Gravel Absent/Sparse (M,OV) Sparse/Moderate (G,BD) Absent/Sparse (BD) Trash/Pasture/ 10 0.7 Glide/Riffle
Riprap/
Bridge
I Fine Gravel Absent/Sparse (M,OV) Sparse/Moderate G,BD) Absent/Sparse (BD) Trash/Pasture/ 12 2.6 Pool
Riprap/
Bridge
J Sand Absent/Sparse (M,OV) Sparse/Moderate (G,BD) Absent/Sparse (BD) Trash/Pasture/ 10 1.4 Pool/Riffle
Riprap/
Bridge
K Sand Absent/Sparse Sparse/Moderate Absent/Sparse Trash/Pasture/ -- -- --
Riprap/
Bridge
Table 11. Rapid habitat assessment ratings for sites on Bear-in-the-Lodge and Black Pipe Creeks.
[O, optimal; SO, sub-optimal; M, marginal; P, poor; --, no data]
Riparian
Epifaunal Vegetative vegetative
Site substrate Velocity/depth Sediment Channel flow Channel Riffle Bank stability protection zone width
number cover Embeddedness regime deposition status alteration frequency right/left right/left right/left
Bear-in-the-Lodge Creek
1 O O O SO O SO SO O/O O/O SO/SO
3 O P M O O O P SO/SO O/O O/O
4 O O O SO SO O O P/M P/M O/O
Black Pipe Creek

5 -- -- -- -- -- -- -- -- -- --
6 O SO O SO SO O O SO/SO O/O O/SO
8 P SO M P P M M SO/SO M/M M/M


Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000-2004

Uploaded by

Copyright:

Available Formats

Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000-2004

Uploaded by

Document Information

Original Title

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Summary of Environmental Monitoring and Assessment Program (EMAP) Activities in South Dakota, 2000-2004

Uploaded by

Copyright:

Available Formats

Summary of Environmental Monitoring and

Assessment Program (EMAP) Activities in

By Allen J. Heakin, Kathleen M. Neitzert, and Jeffrey S. Shearer

Prepared in cooperation with the

Scientific Investigations Report 2006-5007

U.S. Department of the Interior

U.S. Geological Survey

U.S. Geological Survey, Reston, Virginia: 2006

For product and ordering information:

Conversion Factors and Datums

Other abbreviations and acronyms used:

By Allen Heakin1, Kathleen M. Neitzert1, and Jeffrey S. Shearer2

Abstract Relatively early in the EMAP-West stream-assessment

S018 S061 S004 S057

S065 S007 Dry Cr

S061 Site randomly selectedNumber is site number

S108 Dry Cr S113 S097

S114 Candidate reference site Number is site number

Site Latitude Longitude Date(s) visited

Site Latitude Longitude Date(s) visited

Candidate reference sites sampled 20022004

Site Latitude Longitude Date(s) visited

Site Latitude Longitude Date(s) visited

10215' 10200' 10145 10130 10115' 10100' 10045'

Middle White River Basin boundary

yield about 90percent of the fish species present (Reynolds

Substrate Size and Type

insects, algae, and fish. Terrestrial vegetation provides bank

repeated by moving upstream until the gradient between each

Methods for Collecting Vertebrate Data

Quality Assurance and Quality Control

Table 2. Information for sites used to characterize geologic influences.

3 433338101482100 Bear-in-the-Lodge Creek USEPA/EMAP reference site

4 434027101502600 Lower Bear-in-the-Lodge Creek USGS stream assessment site

5 432735101100300 Upper Black Pipe Creek USGS stream assessment site

6 433822101125500 Black Pipe Creek USEPA/EMAP reference site

8 434633101134000 Lower Black Pipe Creek USGS stream assessment site

Water Quality Physical Habitat

FLOW, IN CUBIC FEET PER SECOND

STREAMFLOW, IN CUBIC FEET PER SECOND

DISCHARGE, IN CUBIC FEET PER SECOND

FLOW, IN CUBIC FEET PER SECOND

STREAMFLOW, IN CUBIC FEET PER SECOND

DISCHARGE, IN CUBIC FEET PER SECOND

Figure 18. Upper Black Pipe Creek, assessment sites:

Figure 17. Bear-in-the-Lodge Creek, assessment sites:

U.S. Geological Survey, 19972004, National field manual for

Table 3. General guidelines for consideration in selection of candidate reference sites.

Badlands (parts of White River and some of its tributaries)

Sand Hills (Little White/Keya Paha Rivers)

Western South Dakota shales (Cheyenne/Bad Rivers)

Western South Dakota sandstones/siltstones (Grand/Moreau Rivers)

Missouri River breaks

Upper James River

Lower James/Lower Big Sioux/Vermillion Rivers

Coteau des Prairies

Upper Big Sioux River

5. Long-term viability/security/accessibilityLong-term potential for maintenance in a minimal-influence condition would be beneficial.

Table 4. Data reporting criteria for water chemistry analyses.