Transitions between aquatic and terrestrial environments can be recognized as biogeochemically active ecotones that support high CH4 release. We studied the links between littoral CH4 fluxes and aquatic vegetation, hydrologic conditions, and sediment quality, and integrated the CH4 fluxes into a whole-lake assessment. Methane fluxes were measured using a closed chamber method in the littoral and pelagic zones of three Finnish mid-boreal lakes from May to October. The cumulative CH4 fluxes were spatially integrated over the lake relative to the vegetation coverage in the littoral, and to depth zones in the pelagic regions. During the ice-free period, 66–77% of the CH4 was released from the littoral zone, and the mean CH4 effluxes from these lakes were 0.08–0.42 mol m−2 ice-free season−1. Littoral and pelagic productivity was reflected in CH4 release from the lakes. Our results show that estimates of lake CH4 release should include an assessment of the vegetated littoral zone.