The increasing eutrophication, the introduction of Nile perch (Lates niloticus) and the increasing fishing pressure has changed Lake Victoria tremendously the last century. Since the 1960s, eutrophication increased primary production, enabling an increase in fish production. However, eutrophication also created hypoxia pockets, which reduced the available habitats for fish. In addition, the endemic haplochromines declined, whereas the introduced Nile perch boomed in the 1980s. The Nile perch boom and increased fish production resulted in the largest freshwater fisheries of the world. However, it is unclear whether fish production can still increase with further eutrophication as maximum primary production rates may have been reached. Fish stocks fluctuate since the 1980s and in order to manage these, it is important to understand how eutrophication and fisheries affect the Nile perch population. The present study investigates the bottom-up effects of eutrophication on the Nile perch and food-web dynamics in south-east Lake Victoria. We analysed the level of eutrophication along an eutrophication gradient in the Mwanza Gulf. Phytoplankton biomass varied spatially and seasonally and was limited by nutrients in deep water and by light in shallow water. Fish distributions were dynamic, with environmental factors depth and temperature influencing Nile perch size structure and distribution patterns similarly on small and large spatial scales. Although prey densities of haplochromines and Caridina nilotica shrimp did not explain Nile perch distributions, ontogenetic diet shifts and composition were related to prey densities, suggesting an opportunistic feeding behaviour of Nile perch. Small Nile perch however, showed some preference to shrimp and Nile perch preferred haplochromines above Dagaa (Rastrineobola argentea) and juvenile Nile perch as fish prey. On a food-web level, the base of the food web was spatially and seasonally highly dynamic. The onset of rains caused a spatial differentiation in littoral/benthic and pelagic carbon sources, affecting the whole food web. Trophic levels of fish were related to the spatial variation in diet compositions. Although a large heterogeneity was found in water quality, fish distributions and food-web structure, bottom-up processes affected the food web similarly. Despite the ongoing nutrient load in Lake Victoria, water quality has improved since the 1990s. Climate forcing through increasing wind speeds increased visibility and oxygen levels. Global climate change will therefore be an important driver of the water quality and fish distributions of Lake Victoria.