Cultural eutrophication due to excessive inputs of nutrients seriously threatens aquatic ecosystems worldwide and is one of the major anthropogenic stressors on aquatic biota in European rivers. In streams and shallow rivers, its effects include excessive periphyton growth, which causes biological clogging and thereby oxygen depletion in the hyporheic zone. The result is a serious degradation of habitat quality for benthic invertebrates as well as for the eggs and larvae of gravel-spawning fish. Unlike in standing waters, efficient tools for controlling eutrophication in rivers are lacking. However, top-down control of the food-web by manipulating fish stocks, similar to the biomanipulation successfully applied in lakes, offers a promising approach to mitigating the effects of eutrophication in shallow rivers, especially those in which major reductions in nutrient inputs are not feasible. The overall aim of this thesis was to assess the potential for top-down control by two large cypriniform fish, the common nase (Chondrostoma nasus), the only obligate herbivorous fish species in European rivers, and the omnivorous European chub (Squalius cephalus), to mitigate the effects of eutrophication in medium-sized rivers. I therefore conducted field experiments on different spatial and temporal scales in the hyporhithral zone of a eutrophic gravel-bed river. Generally, the results of those experiments revealed the crucial role of fish-mediated top-down effects in river food webs. In a 4-year reach-scale experiment, the key contribution of my thesis, the enhancement of fish densities significantly increased both oxygen availability and water exchange in the upper layer of the hyporheic zone, even though the top-down effects of the fish on periphyton biomass were relatively small. These findings were supported by those of a 4-week mesocosm experiment, which also provided insights into the mechanisms underlying the mitigation of eutrophication effects by nase and chub. The top-down effects of both fish species reduced hyporheic oxygen depletion, suggesting a reduction of biological clogging. The positive effects of herbivorous nase on hyporheic oxygen availability could be attributed to benthic grazing, whereas the reduction of hyporheic oxygen depletion in the presence of omnivorous chub was best explained by the enhanced bioturbation induced by the fish’s benthic foraging. Overall, the results of my thesis demonstrate that biomanipulation achieved by enhancing herbivorous and omnivorous fish stocks can mitigate the effects of eutrophication in medium-sized European rivers. The results may be the first step towards the establishment of biomanipulation as a supportive management tool for eutrophication control in running waters and therefore as a strategy to preserve aquatic biodiversity.