Northern lakes are important sources of the climate forcing trace gases methane (CH4) and carbon dioxide (CO2). A substantial portion of lakes' annual emissions can take place immediately after ice melt in spring. The drivers of these fluxes are neither well constrained nor fully understood. We present a detailed carbon gas budget for three subarctic lakes, using 6 years of eddy covariance and 9 years of manual flux measurements. We combine measurements of temperature, dissolved oxygen, and CH4 stable isotopologues to quantify functional relationships between carbon gas production and conversion, energy inputs, and the redox regime. Spring emissions were regulated by the availability of oxygen in winter, rather than temperature as during ice‐free conditions. Under‐ice storage increased predictably with ice‐cover duration, and CH4 accumulation rates (25 ± 2 mg CH4‐C·m−2·day−1) exceeded summer emissions (19 ± 1 mg CH4‐C·m−2·day−1). The seasonally ice‐covered lakes emitted 26–59% of the annual CH4 flux and 15–30% of the annual CO2 flux at ice‐off. Reduced spring emissions were associated with winter snowmelt events, which can transport water downstream and oxygenate the water column. Stable isotopes indicate that 64–96% of accumulated CH4 escaped oxidation, implying that a considerable portion of the dissolved gases produced over winter may evade to the atmosphere.