Elevated concentrations of dissolved organic carbon (DOC) promote browning of lakes, which alters the physicochemical properties of water and ecosystem functioning. However, browning‐induced changes in basal production of polyunsaturated fatty acids from the n‐3 and n‐6 families (n‐3 and n‐6 PUFA) in lakes are not fully understood. The concentrations of PUFA, which are micronutrients required to maintain growth and reproduction of consumers, have been suggested to either rise or decline in seston as a response to lake browning. Elevated DOC concentrations may also promote bacterial biomass and production and thus potentially increase the concentration of bacterial fatty acids (BAFA) in seston. We analyzed phytoplankton, bacteria and heterotroph biomasses, the taxonomic composition of phytoplankton, and the concentrations and mass fractions of bioseston PUFA, BAFA, eicosapentaenoic, and docosahexaenoic acids in ten boreal lakes in eastern Finland, with DOC concentration ranging from 2.8 to 18.7 mg/L. Our results showed that the abundance of PUFA in seston depended on the responses of phytoplankton biomass and community composition to lake browning. Lake browning increased seston PUFA and BAFA concentrations (expressed as µg/L) but not the contents (expressed as µg/mg bioseston C). Although low DOC lakes had a favorable phytoplankton community (in terms of PUFA content), the phytoplankton biomass in these oligotrophic lakes was so low that the concentration of PUFA remained low compared to high DOC lakes. The increasing concentration of PUFA in bioseston along the DOC gradient was mainly due to the increasing biomass of nuisance alga Gonyostomum semen . However, Gonyostomum may be too large for small‐sized zooplankton to ingest, and thus, the trophic transfer of PUFA may be impaired. The trajectories for lake browning and the basal production of PUFA also may depend on the source of carbon and associated nutrient loading; DOC and nutrient loading from agricultural areas may promote cyanobacteria dominance and decrease PUFA availability in lakes, while DOC runoff from more acidic and nutrient‐poor peatlands may promote Gonyostomum dominance and increase seston PUFA concentration.