Lakes and reservoirs are important emitters of climate forcing trace gases. Various environmental drivers of the flux, such as temperature and wind speed, have been identified, but their relative importance remains poorly understood. Here we use an extensive field dataset to disentangle physical and biogeochemical controls on the turbulence-driven diffusive flux of methane (CH4) on daily to multi-year timescales. We compare 8 years of floating chamber fluxes from three small, shallow subarctic lakes (2010–2017, n = 1306) with fluxes computed using 9 years of surface water concentration measurements (2009–2017, n = 606) and a small-eddy surface renewal model informed by in situ meteorological observations. Chamber fluxes averaged 6.9 ± 0.3 mg m−2 d−1 and gas transfer velocities (k600) from the chamber-calibrated surface renewal model averaged 4.0 ± 0.1 cm h−1. We find robust (R2 ≥ 0.93, p < 0.01) Arrhenius-type temperature functions of the CH4 flux (Ea' = 0.90 ± 0.14 eV) and of the surface CH4 concentration (Ea' = 0.88 ± 0.09 eV). Chamber derived gas transfer velocities tracked the power-law wind speed relation of the model (k ∝ u3/4). While the flux increased with wind speed, during storm events (U10 ≥ 6.5 m s−1) emissions were reduced by rapid water column degassing. Spectral analysis revealed that on timescales shorter than a month emissions were driven by wind shear, but on longer timescales variations in water temperature governed the flux, suggesting emissions were strongly coupled to production. Our findings suggest that accurate short- and long term projections of lake CH4 emissions can be based on distinct weather- and climate controlled drivers of the flux.