Measurements of CO2 flux between terrestrial surfaces and the atmosphere are warranted to estimate current trends in carbon levels in our atmosphere and soils. In the past century, the introduction of agriculture to the prairies has coincided with a decline in soil carbon and the potential of soils to grow crops. The carbon stored in agricultural soils is not only relevent to agronomy, but also to the mitigation of greenhouse gases as governments move forward with the Kyoto agreement. The focus of our study was to measure CO2 fluxes in an agricultural system common to the Canadian prairies and assess the dynamics of seasonal soil organic matter change. This study was conducted in two adjacent dryland fields where a crop (barley)-fallow rotation was established between 1994-96. Five automated soil chambers were designed to measure soil respiration eight times daily in both fields. In addition, two Bowen ratio units were used to simultaneously monitor gradients of heat, water vapor and CO2 above both fields. The autochambers were shown to be a reliable measure of soil respiration. Carbon dioxide measurements in the fallow field indicated that the autochambers gave similar estimates compared with the Bowen ratio approach. Data from the autochambers showed that soil respiration under barley was double that in fallow. In fallow, the variability in the CO2 flux was best explained by soil moisture and temperature. These factors were not as significant in soil respiration under barley, perhaps because the contribution from root respiration was less sensitive to soil microclimate. Bowen ratio data indicated that respiration from the barley crop was 44 and 32% of gross photosynthesis in 1994 and 1996, respectively. In both years, barley removed CO2 from the atmosphere while the soil gained carbon, however, the amount gained by the soil was less than that removed from the atmosphere due to grain harvest. The loss of carbon in fallow was lower in a dry year than in a wet year. In a wet year, the fallow-barley system was a source of CO2 to the atmosphere. In a dry year, the fallow-crop system removed CO2 from the atmosphere but the soil still lost carbon due to the removal of grain.