Freshwater ecosystems have long been neglected as an important part of the global carbon cycle. However, research shows that most of the world’s lakes are net-heterotrophic and consequently emitters of greenhouse gases to the atmosphere. In many boreal and north-temperate lakes, most of the yearly emissions usually occur in spring, shortly after ice-thaw. The aim of this study was to quantify the flux of carbon dioxide (CO2) and methane (CH4) in three boreal lakes, during this annual event. In order to do this, water samples were collected before and after ice-thaw, and the flux was estimated as the difference in mass of carbon between the two sampling occasions. The results showed that the lakes had accumulated high amounts of carbon over the winter, with higher concentrations generally at higher depths. The fluxes during ice-thaw ranged from 234–380 (mean: 302) and -1.15–15.12 (mean: 8.64) mmol m-2 y-1 for CO2 and CH4, respectively. Given their small sizes, the lakes emitted less carbon, per unit area, than expected. This was assumed to be due to the lakes’ rather isolated locations and since the heating of the water rapidly caused them to become highly stratified, thus preventing the wind from releasing deeper stored carbon. Presumably, this holds true for other similar boreal lakes as well, which suggests that attention – in such ecosystems – also needs to be brought to other mixing periods.