Fish play a key role in the trophic dynamics of lakes. With climate warming, complex changes in fish assemblage structure may be expected owing to direct effects of temperature and indirect effects operating through eutrophication, water level changes, stratification and salinisation. We reviewed published and new long-term (10–100 years) fish data series from 24 European lakes (area: 0.04–5,648 km²; mean depth: 1–177 m; a north–south gradient from Sweden to Spain). Along with an annual temperature increase of about 0.15–0.3°C per decade profound changes have occurred in either fish assemblage composition, body size and/or age structure during recent decades and a shift towards higher dominance of eurythermal species. These shifts have occurred despite a reduction in nutrient loading in many of the lakes that should have benefited the larger-sized individuals and the fish species typically inhabiting cold-water, low-nutrient lakes. The cold-stenothermic Arctic charr has been particularly affected and its abundance has decreased in the majority of the lakes where its presence was recorded. The harvest of cool-stenothermal brown trout has decreased substantially in two southern lakes. Vendace, whitefish and smelt show a different response depending on lake depth and latitude. Perch has apparently been stimulated in the north, with stronger year classes in warm years, but its abundance has declined in the southern Lake Maggiore, Italy. Where introduced, roach seems to take advantage of the higher temperature after years of low population densities. Eurythermal species such as common bream, pike–perch and/or shad are apparently on the increase in several of the lakes. The response of fish to the warming has been surprisingly strong and fast in recent decades, making them ideal sentinels for detecting and documenting climate-induced modifications of freshwater ecosystems.