The technologies of sonar and laser scanning are an efficient and widely used source of spatial information with regards to underwater and over ground environment respectively. The measurement data are usually available in the form of groups of separate points located irregularly in three-dimensional space, known as point clouds. This data model has known disadvantages, therefore in many applications a different form of representation, i.e. 3D surfaces composed of edges and facets, is preferred with respect to the terrain or seabed surface relief as well as various objects shape. In the paper, the authors propose a new approach to 3D shape reconstruction from both multibeam and LiDAR measurements. It is based on a multiple-step and to some extent adaptive process, in which the chosen set and sequence of particular stages may depend on a current type and characteristic features of the processed data. The processing scheme includes: 1) pre-processing which may include noise reduction, rasterization and pre-classification, 2) detection and separation of objects for dedicated processing (e.g. steep walls, masts), and 3) surface reconstruction in 3D by point cloud triangulation and with the aid of several dedicated procedures. The benefits of using the proposed methods, including algorithms for detecting various features and improving the regularity of the data structure, are presented and discussed. Several different shape reconstruction algorithms were tested in combination with the proposed data processing methods and the strengths and weaknesses of each algorithm were highlighted.