* Biogenic methane as an alternative carbon and energy source for freshwater organisms has been receiving increasing attention, but the phenomenon is still poorly understood for shallow lakes. We measured the carbon and nitrogen stable isotope signatures (δ13C, δ15N) for key groups of pelagic and benthic organisms, including crustacean zooplankton, chironomid larvae, young-of-the-year and adult fish, to assess whether biogenic methane contributes to pelagic and benthic food webs in a large, shallow lake, Lake Võrtsjärv, Estonia. * In the southern part of the lake, covered by macrophytes, crustacean zooplankton showed strong seasonal variation of δ13C, with the lowest values occurring in the period of oxygen depletion. Chironomid (Chironomus plumosus) larvae showed high isotopic variability within the lake, with strongly 13C-depleted and 15N-depleted signatures (down to δ13C −64.0‰ and δ15N −2.6‰) in the macrophyte-covered area. * Our results indicate that carbon derived from biogenic methane can contribute seasonally to the benthic food web and, to some extent, also to the pelagic food web, where the lake is covered by macrophytes. Moreover, δ13C values for roach (Rutilus rutilus), perch (Perca fluviatilis) and pike (Esox lucius) from the macrophyte-dominated area were on average 3.5‰ lower than those for the same fish from the plankton-dominated lake area, suggesting some carbon derived from methane is transferred up through the food web. * Although no direct evidence is available, our results, together with previous studies of the lake, suggest that protozoans could be a potentially important link from methane-oxidising bacteria to animals higher in the web.