Surface water pCO2 and pCH4 measurements were made in Québec (Canada) during consecutive seasons from 2006 to 2008 in two boreal reservoirs and nearby lakes. The goal of this follow-up was to evaluate greenhouse gas emissions from the water bodies studied, through flux calculations using the Thin Boundary Layer Model. Our measurements underscored the winter CO2 accumulation due to ice cover and the importance of a reliable estimation of spring diffusive emissions as the ice breaks up. We clearly demonstrated that in our systems, CH4 diffusive fluxes (in terms of CO2 equivalent) were of minor importance in the GHG emissions, with CO2 diffusive fluxes generally representing more than 95% of the annual diffusive fluxes. We also noted the extent of CO2 spring diffusive emissions (16% to 52%) in the annual budget.