Eutrophication and rising water temperature in freshwaters may increase the total production of a lake while simultaneously reducing the nutritional quality of food web components. We evaluated how cyanobacteria blooms, driven by agricultural eutrophication (in eutrophic Lake Köyliöjärvi) or global warming (in mesotrophic Lake Pyhäjärvi), influence the biomass and structure of phytoplankton, zooplankton, and fish communities. In terms of the nutritional value of food web components, we evaluated changes in the ω-3 and ω-6 polyunsaturated fatty acids (PUFA) of phytoplankton and consumers at different trophic levels. Meanwhile, the lakes did not differ in their biomasses of phytoplankton, zooplankton, and fish communities, lake trophic status greatly influenced the community structures. The eutrophic lake, with agricultural eutrophication, had cyanobacteria bloom throughout the summer months whereas cyanobacteria were abundant only occasionally in the mesotrophic lake, mainly in early summer. Phytoplankton community differences at genus level resulted in higher arachidonic acid, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) content of seston in the mesotrophic than in the eutrophic lake. This was also reflected in the EPA and DHA content of herbivorous zooplankton (Daphnia and Bosmina) despite more efficient trophic retention of these biomolecules in a eutrophic lake than in the mesotrophic lake zooplankton. Planktivorous juvenile fish (perch and roach) in a eutrophic lake overcame the lower availability of DHA in their prey by more efficient trophic retention and biosynthesis from the precursors. However, the most efficient trophic retention of DHA was found with benthivorous perch which prey contained only a low amount of DHA. Long-term cyanobacterial blooming decreased the nutritional quality of piscivorous perch; however, the difference was much less than previously anticipated. Our result shows that long-term cyanobacteria blooming impacts the structure of plankton and fish communities and lowers the nutritional quality of seston and zooplankton, which, however, is mitigated at upper trophic levels.