An automated 6-chamber system designed to make continuous measurements of soil carbon dioxide efflux and biotic respiration is used to study the diurnal and seasonal courses of autotrophic and heterotrophic respiration in a 121-year-old black spruce and a 73-year-old aspen forest located near southern boreal treeline in Saskatchewan, Canada. Each chamber system has been operational since July 2000 as part of the Boreal Ecosystem and Monitoring Sites (BERMS) program and has provided a strong temporal resolution of respiration. Here, we examine the temporal and spatial variability in soil surface carbon dioxide effluxes and the seasonal variation in tree bole respiration to show how these vary with climate and phenology. The significant contribution of wintertime carbon losses is also discussed. Annual ecosystem respiration is estimated from both chamber and eddy covariance approaches to address the uncertainty in eddy covariance annual carbon budget estimates, which can be related to poor eddy flux quality resulting from low nighttime friction velocity above tall vegetation.