Morphological in physical processes in rivers, which develop on river catchment scale, play an important role for the ecological status of rivers. This work aims to compare the legal circumstances, objectives, competences and methodologies in the assessment of the ecological quality of running waters in Switzerland and France, in order to be able to identify ecologically sensitive river sections. The analysis focuses therefor on the assessment of the hydromorphology and the protection of river habitats. To compare the different national approaches the catchment of the Rhone River was chosen as case study. Aims, competences, assessment methods and methods to designate ecologically sensitive river sections were determined based on a research of legislative texts, scientific literature and publications of the appropriate authority. In Switzerland protection of running waters is bound to political units, in France to environmental units. Framework conditions and aims are regulated by federal laws; in the single cantons the methodology may differ partly even because of related cantonal laws. The aims are not defined by an evaluation pattern and refer to a reference water body or model like in France, but determine room for interpretation. Data concerning the assessment of ecological quality are just present for the French part of the Rhone Catchment; a Swiss way of assessing ecological quality of running waters by a number of quality elements is just being tested. Data regarding the hydromorphology is extensively available for the whole catchment. Plus, both countries designate protection areas with similar protection aims regarding habitats and species. Regarding all this ecologically sensitive river sections could be identified based on available data, whereby completeness could be achieved by the implementation of an assessment method regarding ecologic quality in Switzerland.