Through cascading effects within lake food webs, commercial and recreational fisheries may indirectly affect the abundances of organisms at lower trophic levels, such as phytoplankton, even if they are not directly consumed. So far, interactive effects of fisheries, changing trophic state and climate upon lake ecosystems have been largely overlooked. Here we analyse case studies from five European lake basins of differing trophic states (Lake Vortsjarv, two basins of Windermere, Lake Geneva and Lake Maggiore) with long-term limnological and fisheries data. Decreasing phosphorus concentrations (re-oligotrophication) and increasing water temperatures have been reported in all five lake basins, while phytoplankton concentration has decreased only slightly or even increased in some cases. To examine possible ecosystem-scale effects of fisheries, we analysed correlations between fish and fisheries data, and other food web components and environmental factors, Re-oligotrophication over different ranges of the trophic scale induced different fish responses. In the deeper lakes Geneva and Maggiore, we found a stronger link between phytoplankton and planktivorous fish and thus a more important cascading top-down effect than in other lakes. This connection makes careful ecosystem-based fisheries management extremely important for maintaining high water quality in such systems. We also demonstrated that increasing water temperature might favour piscivores at low phosphorus loading, but suppresses them at high phosphorus loading and might thus either enhance or diminish the cascading top-down control over phytoplankton with strong implications for water quality.