The Fe (oxyhydr)oxide rind, or Fe plaque, that forms on aquatic plant roots is an important sorbent of metal(loid)s and plays a role in the attenuation of metal(loid) uptake into higher plants. However, the mineral composition of Fe plaque and thus its potential to sorb metal(loid)s is affected by solution chemistry. The predominant strategy to characterize Fe plaque using dithionite-citrate-bicarbonate (DCB) extraction and elemental analysis reveals total Fe quantity but misses the mineral structure of the Fe (oxyhydr)oxide. Here, we developed a new technique using gentle sonication to sample intact Fe plaque from the root system and concentrate it for subsequent mineralogical characterization using synchrotron-based X-ray diffraction and X-ray absorption spectroscopy. We then coupled that data with conventional DCB extraction. The sample preparation method was effective at concentrating As-bound Fe plaque minerals in a uniform coating onto membranes that could easily be analyzed with X-ray techniques. Using these methods, we show that the percentage of poorly ordered Fe minerals in Fe plaque increases with increasing pore-water Si in flooded rice paddy soils. These findings have implications for understanding mineral controls on As cycling in the soil-rice nexus, and the sampling approach can be adopted for other aquatic plant systems.