Emission of greenhouse gases (GHGs) from inland waters is recognized as highly important and an understudied part of the terrestrial carbon (C) biogeochemical cycle. These emissions are still poorly quantified in subarctic regions that contain vast amounts of surface C in permafrost peatlands. This is especially true in NE European peatlands, located within sporadic to discontinuous permafrost zones which are highly vulnerable to thaw. Initial measurements of C emissions from lentic waters of the Bolshezemelskaya Tundra (BZT; 200,000 km2) demonstrated sizable CO2 and CH4 concentrations and fluxes to the atmosphere in 98 depressions, thaw ponds, and thermokarst lakes ranging from 0.5 × 106 to 5 × 106 m2 in size. CO2 fluxes decreased by an order of magnitude as waterbody size increased by > 3 orders of magnitude while CH4 fluxes showed large variability unrelated to lake size. By using a combination of Landsat‐8 and GeoEye‐1 images, we determined lakes cover 4% of BZT and thus calculated overall C emissions from lentic waters to be 3.8 ± 0.65 Tg C yr−1 (99% C‐CO2, 1% C‐CH4), which is two times higher than the lateral riverine export. Large lakes dominated GHG emissions whereas small thaw ponds had a minor contribution to overall water surface area and GHG emissions. These data suggest that, if permafrost thaw in NE Europe results in disappearance of large thermokarst lakes and formation of new small thaw ponds and depressions, GHG emissions from lentic waters in this region may decrease.