1. It has long been known that substantial amounts of methane are produced in anoxic lake sediments, and the components of the methane cycle in lakes have been well described. At oxic–anoxic interfaces, methane-oxidising bacteria (MOB) convert methane to microbial biomass and can be highly productive. However, only recently has methane been recognised as a potentially important carbon and energy source for lake food webs, and some instances have also been reported of methane contribution to river food webs. Stable isotope analysis (SIA) has provided compelling evidence in this respect and has been supplemented by other lines of evidence. 2. In the benthic food webs of lakes, profundal chironomid larvae appear to be the main conduits for trophic transfer of biogenic methane via grazing on MOB. The mode of feeding of these larvae and the microhabitats they generate both promote larval ability to exploit MOB production. Support to chironomid larvae from methane is rather widespread, but its degree is highly variable; estimates suggest that in some lakes methane-carbon might contribute more than 60% of chironomid carbon biomass. 3. Evidence of crustacean zooplankton in lakes deriving part of their carbon from methane is currently more limited. Reports from some lakes have indicated Daphnia with a substantial (>50%) contribution of methane-carbon in their biomass. However, for this to happen, an oxic–anoxic interface where sufficient MOB production can occur needs to be within the range of vertical migrations by zooplankton, which may only rarely be the case. Hence, a significant methane subsidy of pelagic food webs in lakes is probably much less widespread than for benthic food webs. 4. There is also recent and currently very limited evidence that some stream benthos derives biomass carbon (reported values up to 30%) from methane. This can occur in stagnant backwater pools where conditions can be analogous to those in lake sediments. However, groundwater aquifers can also supply water supersaturated with methane to some rivers, providing a basis for a microbially-mediated transfer of methane-carbon to river benthos. 5. Evidence for significant transfer of methane-derived carbon to higher trophic levels is still very limited. Within some lakes, those fish species that feed extensively on chironomid larvae can derive a substantial part (perhaps up to 20%) of their carbon biomass from methane. It is also likely that methane-carbon produced in lakes or rivers is exported to riparian ecosystems when emerging chironomids or other insects are eaten by invertebrate or avian predators. 6. We argue that conceptual models of freshwater food webs, and especially those for lakes, need to be modified to enable incorporation of biogenic methane as a carbon and energy source. For some types of lakes, carbon and energy budgets certainly need to take account of the production and utilisation of biogenic methane, and the accumulating evidence indicates that this is a more widespread phenomenon that has generally been acknowledged hitherto.