We conducted a fish survey in 40 lakes in western and central Turkey. Fifty species (one to eleven per lake) were recorded, including eighteen endemic and seven alien species. We investigated which local geo-climatic and other environmental variables shaped the fish assemblages. Altitude and temperature turned out to be the most important factors for total species richness as well as richness of omnivorous and zooplanktivorous species and the Shannon-Wiener diversity index, with more species and higher diversity occurring in the warmer lowland lakes. Altitude may affect the fish assemblage directly through dispersal limitation or indirectly by creating a gradient in temperature with which it was strongly correlated. Cyprinidae was the most species-rich and widespread family. Atherinidae, Gobiidae, and Mugilidae (families of marine origin) were mainly found in the lowland regions, while Salmonidae exclusively appeared in the high-altitude lakes. The presence of widely distributed translocated native and alien species revealed a large human impact on the fish assemblages, potentially threatening the rich endemic fish fauna in lakes in this region.