Small thermokarst lakes release greenhouse gases (GHGs) as permafrost thaws, but most studies focus on diurnal measurements, potentially overlooking significant variations. We measured GHG fluxes from two lakes in Nunavik over two summers – one colder, one warmer – alongside 2 years of continuous water column monitoring. Fluxes were higher in the warmer summer, with strong day–night differences. Our findings show that accurate GHG estimates require full diel measurements and seasonal considerations.