Freshwater ecosystems are exposed to a multitude of anthropogenic stressors, such as overexploitation, water pollution, hydro-morphological alteration and hydropower operations. Further, it is very likely that we will see a global surge in the construction of small to medium-sized hydropower plants located in mountainous regions. The impact of such small hydropower plants are most obvious in the downstream river reaches which experience reduced flows and sediment inputs below the water takes. The resulting deterioration of the in-stream habitat within these residual flow reaches has been shown to impact on fish density and condition, invertebrate and fish community composition and ecosystem functioning such as organic matter breakdown and retention. But we currently lack an understanding of the underlying mechanisms affecting food-web structure and dynamics. Therefore we are investigating in-stream conditions and the structure and functioning of food-webs along the river reaches impacted by small run-of-river hydropower plants. The knowledge we gain will then help designing efficient mitigation measures.