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We used stable carbon (δ13C) and nitrogen (δ15N) isotopes to assess the importance of benthic algae for the zooplankton individual growth in winter in a shallow, clear subarctic lake. The δ13C values of calanoid (Eudiaptomus graciloides) and cyclopoid (Cyclops scutifer) zooplankton in autumn suggest a food resource of pelagic origin during the ice-free period. The zooplankton δ13C values were high in spring compared to autumn. E. graciloides did not grow over winter and the change in δ13C was attributed to a decrease in lipid content during the winter. In contrast, the increase in δ13C values of C. scutifer over the winter was explained by their growth on organic carbon generated by benthic algae. The δ15N of the C. scutifer food resource during winter was low compared to δ15N of the benthic community, suggesting that organic matter generated by benthic algae was mainly channelled to zooplankton via 15N-depleted heterotrophic bacteria. The results demonstrate that benthic algae can sustain zooplankton metabolic demands and growth during long winters, which, in turn, may promote zooplankton growth on pelagic resources during the summer. Such multi-chain omnivory challenges the view of zooplankton as mainly dependent on internal primary production and stresses the importance of benthic resources for the productivity of plankton food webs in shallow lakes.