* We aimed to distinguish the relative contributions of natural and anthropogenic local factors on patterns of fish diversity in European lakes at different geographical scales. * We compiled data from standardised fish monitoring using multimesh benthic gill nets, information on lake morphometry and on geographical, climatic and anthropogenic pressure variables from 1632 lakes in 11 European countries. By means of regression trees, we determined those natural and anthropogenic factors and their thresholds that best predicted local fish diversity, density and mean size. Generalised linear models were used to assess the influence of anthropogenic factors at smaller geographical and morphometric scales. * Local fish species richness and diversity were related mainly to morphometric and (bio)geographical/climatic variables. Larger and deeper lakes in warm areas tended to be the most species rich and diverse. Fish density was related mainly to anthropogenically driven productivity but also was sensitive to geographical/climatic factors. Thus, warmer and shallower lower-altitude European lakes, which are usually more eutrophic, had higher fish densities than cold and deeper higher-altitude lakes. Fish size increased with altitude and declined with increasing seasonality and temperature. * After controlling for the natural factors, productivity had a positive effect on fish species richness and diversity, whereas it negatively influenced fish size. * Our results suggest that macroecological patterns of lake fish diversity across Europe are best predicted by natural factors. The contribution of anthropogenic factors to fish diversity was evident only via the effect of eutrophication at smaller geographical scales, whereas no effect could be found from hydromorphological pressures. From an applied perspective, these results suggest that bioassessment and biodiversity evaluation might be most effectively conducted and interpreted locally, where anthropogenic effects on biodiversity become more apparent. At a macroecological scale, the strong effect of environmental temperature on most components of fish diversity suggests future changes in fish diversity as a consequence of climate change.