Based upon well-known relations between abiotic and biotic components of river systems, habitat assessment can serve as an indirect procedure to evaluate the ecological integrity by demonstrating the degree of man-induced alterations of the physical environment. Detailed habitat analysis has been an integral part of aut- or synecological investigations in aquatic environments. In many countries, however, the assessment of the physical environment on a larger spatial scale has become a regular part of watershed management programmes. A primary methodological aspect of large-scale habitat assessment is the selection and definition of evaluation criteria specifically designed to identify key functions and processes of intact river systems. Therefore, special emphasis has to be given to integrative parameters, that reflect the spatial and temporal dynamics of running waters as well as the interactions between rivers and their wetlands. Four groups of evaluation criteria are discussed within the framework of their relevance for aquatic biocoenoses and their validity to identify severe human impacts on running water ecosystems: (1) discharge regime; (2) morphological character; (3) lateral connectivity and (4) longitudinal corridor.