Similar nonsteady-state automated chamber systems were used to measure and partition soil CO2 efflux in contrasting deciduous (trembling aspen) and coniferous (black spruce and jack pine) stands located within 100 km of each other near the southern edge of the Boreal forest in Canada. The stands were exposed to similar climate forcing in 2003, including marked seasonal variations in soil water availability, which provided a unique opportunity to investigate the influence of climate and stand characteristics on soil CO2 efflux and to quantify its contribution to the net ecosystem CO2 exchange (NEE) as measured with the eddy-covariance technique. Partitioning of soil CO2 efflux between soil respiration (including forest-floor vegetation) and forest-floor photosynthesis showed that short- and long-term temporal variations of soil CO2 efflux were related to the influence of (1) soil temperature and water content on soil respiration and (2) below-canopy light availability, plant water status and forest-floor plant species composition on forest-floor photosynthesis. Overall, the three stands were weak to moderate sinks for CO2 in 2003 (NEE of −103, −80 and −28 g C m−2 yr−1 for aspen, black spruce and jack pine, respectively). Forest-floor respiration accounted for 86%, 73% and 75% of annual ecosystem respiration, in the three respective stands, while forest-floor photosynthesis contributed to 11% and 14% of annual gross ecosystem photosynthesis in the black spruce and jack pine stands, respectively. The results emphasize the need to perform concomitant measurements of NEE and soil CO2 efflux at longer time scales in different ecosystems in order to better understand the impacts of future interannual climate variability and vegetation dynamics associated with climate change on each component of the carbon balance.