Methane emissions from the boreal-Arctic region are likely to increase due to warming and permafrost thaw, but the magnitude of increase is unconstrained. Here we show that distinguishing several wetland and lake classes improves our understanding of current and future methane emissions. Our estimate of net annual methane emission (1988–2019) was 34 (95% CI: 25–43) Tg CH₄ yr⁻¹, dominated by five wetland (26 Tg CH₄ yr⁻¹) and seven lake (5.7 Tg CH₄ yr⁻¹) classes. Our estimate was lower than previous estimates due to explicit characterization of low methane-emitting wetland and lake classes, for example, permafrost bogs, bogs, large lakes and glacial lakes. To reduce uncertainty further, improved wetland maps and further measurements of wetland winter emissions and lake ebullition are needed. Methane emissions were estimated to increase by ~31% under a moderate warming scenario (SSP2-4.5 by 2100), driven primarily by warming rather than permafrost thaw.