We studied the interannual variation of surface water partial pressure of CO2 (pCO2) and the CO2 emissions from the 37 large Finnish lakes linking them to the water quality, catchment and climate attributes in 1996–2001. The lake water CO2 was measured three times a year in the study lakes in 1998 and 1999 and for the rest of the years the CO2 was modeled by measured alkalinity. The median annual CO2 emission to the atmosphere ranged between 1.49 and 2.29 mol m−2 a−1. The annual CO2 emission followed closely the annual precipitation pattern with the highest emission during the years when the precipitation was highest (r2=0.81–0.97, P<0.05). There was a strong negative correlation (r2=0.50–0.82, P<0.001) between O2 and CO2 saturation in the lake water during stratification suggesting effective decomposition of organic matter in the lakes. Furthermore, total phosphorus and the proportion of agricultural land in the catchment had significant positive correlations with CO2 saturation.