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.