We evaluated the hypothesis that CO2 uptake by a subalpine, coniferous forest is limited by cool temperature during the growing season. Using the eddy covariance approach we conducted observations of net ecosystem CO2 exchange (NEE) across two growing seasons. When pooled for the entire growing season during both years, light-saturated net ecosystem CO2 exchange (NEEsat) exhibited a temperature optimum within the range 7–12°C. Ecosystem respiration rate (Re), calculated as the y-intercept of the NEE versus photosynthetic photon flux density (PPFD) relationship, increased with increasing temperature, causing a 15% reduction in net CO2 uptake capacity for this ecosystem as temperatures increased from typical early season temperatures of 7°C to typical mid-season temperatures of 18°C. The ecosystem quantum yield and the ecosystem PPFD compensation point, which are measures of light-utilization efficiency, were highest during the cool temperatures of the early season, and decreased later in the season at higher temperatures. Branch-level measurements revealed that net photosynthesis in all three of the dominant conifer tree species exhibited a temperature optimum near 10°C early in the season and 15°C later in the season. Using path analysis, we statistically isolated temperature as a seasonal variable, and identified the dynamic role that temperature exhibits in controlling ecosystem fluxes early and late in the season. During the spring, an increase in temperature has a positive effect on NEE, because daytime temperatures progress from near freezing to near the photosynthetic temperature optimum, and Re values remain low. During the middle of the summer an increase in temperature has a negative effect on NEE, because inhibition of net photosynthesis and increases in Re. When taken together, the results demonstrate that in this high-elevation forest ecosystem CO2 uptake is not limited by cool-temperature constraints on photosynthetic processes during the growing-season, as suggested by some previous ecophysiological studies at the branch and needle levels. Rather, it is warm temperatures in the mid-summer, and their effect on ecosystem respiration, that cause the greatest reduction in the potential for forest carbon sequestration.