Characteristics of French water bodies and fish fauna are described with special reference to physically altered streams. Recent researches on fish physical habitat have produced new insights on: models of probability of fish distributions at a watershed scale, fish ecology, in particular about their habitat preferences, hydraulic statistical modelling with simplification of data collection, models of impacts of flow or modifications to stream morphology, and coupling physics and biology. These models have been validated at fish population (trout) or assemblage (Rhône river) level.Other complementary researches are dealing with fluvial dynamics necessary to maintain habitat or with ecological dynamic linked to flows and morphology (especially substrate).For the legal point of view, Fishing law (1984 in FCE a), Water law (1992 in FCE b), and the last European Water Framework Directive (2000) defined the limits of hydrosystems utilization. They defended the principle of an equilibrium between hydrosystems utilization.It is also necessary to better link streams and their watersheds. Waterbodies regionalization will be a good way to reduce the natural variability of physical and biological situations in order to better manage ecological entities with respect of their sensitivity. The setting of a national survey of fish communities is fundamental.National conservation programmes with main protected areas of France has not been very successful at protecting freshwater fish. Rehabilitation plans of some emblematic fish species Salmon, Sturgeon, Eel, Shad have helped to coordinate actions in large heavily anthropised rivers. In other numerous aquatic systems, it is better to restore the functioning of the first key compartments, hydrology and morphology. Fish communities are in these cases good measures of the benefits of rehabilitation actions. Future research will deal with different interfaces between physics and biology, in order to better manage channels, sediments, flows, and riparian vegetation.