Summary Shallow lakes are important components of the biosphere, but they are also highly vulnerable to damage from human activities in their catchments, such as nutrient pollution. They may also be particularly vulnerable to current warming trends. Forty‐eight tanks were used to create 3‐m3 mesocosms of shallow lake communities, in which the effects of warming by 4 °C and regular nutrient loading at two levels relevant to current degrees of eutrophication were studied in the presence and absence of fish. Warming changed concentrations of soluble phosphate, total nitrogen and conductivity, increased total plant biomass and decreased the amount of phytoplankton through shading by floating plants. Nutrient additions decreased total plant biomass but increased floating plant biomass. Nitrogen increase and warming increased floating plant biomass and decreased plant species richness. The plant community remained intact and did not switch to the turbid‐water, phytoplankton‐dominated community often predicted to be a consequence of global warming and eutrophication. Synthesis and applications. Likely future temperature increase will exacerbate some, but not all symptoms of eutrophication in shallow lakes. Alone it will not cause a switch from plant‐dominated to algal‐dominated systems, but may result in nuisance growths of floating lemnids. Currently underplayed, nitrogen loading should be taken more seriously in the management of European freshwaters.