In running water, the main natural factor of disturbance is hydraulic. Investigation of its biological impact is currently complicated by the increase of anthropogenic disturbances which tend to mask the natural functioning of rivers. Monitoring of the impacts of the artificial alterations undergone by the Middle Rhone River for some decades took place in the mid-1980s. Discharge and temperature could constitute the major events controlling the biological dynamics in terms of variations in species richness, diversity, and abundance. The between-years changes of the structure and diversity of macroinvertebrate communities were connected with the amplitude of discharge fluctuations. This was in accordance with the disturbance-diversity concept and it seems to confirm the intermediate disturbance hypothesis. The fish community mainly depended on hydroclimatic factors that influenced breeding success. Variations in nutrient input played a secondary role in controlling changes in some communities (particularly the periphyton). Therefore it appears that the study of long-term changes in river systems, including the dynamics of their biological communities, requires continuous observations and data collection that only medium- to long-term studies can provide, implying the setting up of ecological monitoring centres for the natural environment such as the Long Term Ecological Research (LTER) sites in United.