The beta diversity among lakes is affected by natural environmental sorting, dispersal constraints, and anthropogenic disturbances. We hypothesized that fish beta diversity would increase towards lower latitudes and be higher in less disturbed lakes at within-region scale, but environmental disturbances could affect these patterns due to community homogenization or heterogenization (e.g., gain of exotic species) among lakes. We used generalized dissimilarity modeling to assess the relative importance of geographic distance, climate, and environmental heterogeneity on fish beta diversity across Denmark, Belgium/The Netherlands, and Spain. We also tested whether differences in beta diversity changed between lake types (e.g., clear vs. turbid lakes and lakes with vs. without exotics fish) within-region and across latitude. Beta diversity increased from Denmark to Spain and geographic distance and climate variability were the main drivers of community change across latitude, but the rate of change varied between lake types. At the within-region scale, factors such as turbidity, lake size, and presence of exotics had varying impacts on beta diversity (i.e., increasing, decreasing, or no effect) across the three regions. Our findings suggest that understanding the effects of environmental disturbances on beta diversity requires consideration of both biogeographic and local factors.