Annual emissions of (CH4 + CO2) to the atmosphere were proportional to net hydrologic inputs of C, mostly by groundwater, at two lakes in the Shingobee River watershed in north-central Minnesota. Williams Lake (WL), a closed basin lake near the top of the watershed, had a hydraulic residence time of 2-4 yr and groundwater exchange of about +2 mol dissolved inorganic carbon (DIC) and -0.1 mol dissolved organic carbon (DOC) m-2 lake area yr-1. The Shingobee River flows through Shingobee Lake (SL) that had a hydraulic residence of 0.3-0.4 yr and received net groundwater plus surface-water inputs of +5.3 to +7.3 mol DIC and fewer than +1.3 mol (DOC + particulate organic carbon) m-2 yr-1. Approximately 60-80% of net annual C input to SL was from groundwater. Lake storage of CH4 and CO2 was greatest in late winter, with maximum emissions to the atmosphere immediately following ice melt. The lakes emitted CH4 continuously during open water, having annual losses of -1.6 mol CH4 m-2 yr-1 at WL and -1.9 mol CH4 m-2 yr-1 at SL. Although the WL epilimnion was CO2 depleted throughout summer, net annual CO2 exchange with the atmosphere was near zero because springtime emission offset summertime uptake. CO2 supersaturation resulted in emission of -8.0 mol CO2 m-2 yr-1 at SL.