Abstract – Fishing is a potent ecological force. In Lake Victoria, East Africa, Nile perch, Lates niloticus contributes to a multi-million dollar fishing industry but is threatened by over-exploitation. We quantified spatial and temporal trends in the distribution, diet and size of Nile perch in Lake Nabugabo, Uganda, a satellite of Lake Victoria. From 1995 to 2007, we detected a decline in catch per unit effort of Nile perch, a shift in their distribution and diet, and a decrease in their body size. A greater proportion of Nile perch were found near wetland ecotones than in the 1990s. This may reflect intensive size-selective fishing in open waters, and encroachment of Vossia cuspidata, an emergent macrophyte that has expanded across the lakeshore. Results highlight the strength of fishing in inducing phenotypic changes in target stocks as well as large-scale changes to the aquatic community and are of value in understanding changes in Lake Victoria.