© 2022 The AuthorsClimate change and eutrophication are among the main stressors of shallow freshwater ecosystems, and their effects on phytoplankton community structure and primary production have been studied extensively. However, their combined effects on the algal production of polyunsaturated fatty acids (PUFA), specifically, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are currently unresolved. Moreover, the proximate reasons for changes in phytoplankton EPA and DHA concentrations are unclear, i.e., the relative importance of ecological (changes in the community composition) vs. ecophysiological (within taxa changes in EPA and DHA levels) factors. We investigated the responses of phytoplankton EPA and DHA concentrations to warming (IPCC climate scenario) and nutrient additions in mesocosms which had been run continuously at varying temperature and nutrient levels for 15 years prior to this study. Nutrient treatment had a significant effect on phytoplankton EPA and DHA concentrations and about 59 % of the variation in EPA and DHA concentrations could be explained by changes in the phytoplankton community structure. Increased biomass of diatoms corresponded with high EPA and DHA concentrations, while cyanobacteria/chlorophyte dominated mesocosm had low EPA and DHA concentrations. Warming had only a marginal effect on the EPA and DHA concentrations in these mesocosms. However, a significant interaction was observed with warming and N:P ratio. Our findings indicate that direct nutrient/temperature effects on algal physiology and PUFA metabolism were negligible and the changes in EPA and DHA concentrations were mostly related to the phytoplankton community structure and biomass. These results also imply that in shallow temperate lakes eutrophication, leading to increased dominance of cyanobacteria, will probably be a greater threat to phytoplankton EPA and DHA production than warming. EPA and DHA are nutritionally important for upper trophic level consumers and decreased production may impair secondary production.