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Soil CO2 efflux is a large respiratory flux from terrestrial ecosystems and a critical component of the global carbon (C) cycle. Lack of process understanding of the spatiotemporal controls on soil CO2 efflux limits our ability to extrapolate from fluxes measured at point scales to scales useful for corroboration with other ecosystem level measures of C exchange. Additional complications are introduced by the effects of soil water content seasonality and rainfall on the performance of measurement techniques. In this paper we present measurements of soil CO2 efflux made at two contrasting sites within a characteristic subalpine forest of the northern Rocky Mountains. Comparison of measurements between the soil respiration chamber technique and the soil CO2 profile technique over daily and seasonal time scales indicated that soil water content plays a major role in the magnitude and seasonality of soil CO2 efflux, especially after snowmelt or following summer rainfall. Agreement between both techniques was limited during high soil water content conditions and after summer rainfall. Differences in diel hysteresis patterns of soil CO2 efflux between sites were controlled by the effects of canopy cover and temporal differences in photosynthetic activity of vegetation. Our results indicate that an accurate parameterization of soil water content heterogeneity in space and time must be a critical component of realistic model representations of soil CO2 efflux from heterogeneous landscapes.