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Daily and seasonal CO2-exchange dynamics between the boundary layer and biosphere is important to understanding Net Ecosystem Exchange of terrestrial ecosystems. Spatial and temporal variations of CO2 fluxes across midwestern cropping systems have not been well documented. This study was designed to monitor and evaluate spatial and temporal dynamics of CO2 exchange across a watershed region for typical production fields of corn (Zea mays L.) and soybean [Glycine max (L.) Merr.] in the Midwest by quantifying the above-canopy, within-canopy, and soil components of C balance for this cropping system. An energy-balance approach using eddy covariance was utilized across different fields making year-around measurements in both corn and soybean fields to quantify the exchange of CO2 and H2O between the crop canopy and the atmospheric boundary layer. Within-canopy concentrations of CO2 and H2O vapor were measured with an eight-port CO2/H2O infrared analyzer. Soil respiration was quantified using soil chambers at various landscape positions throughout the growing season. Fluxes of CO2 and H2O vapor throughout the day were dependent on net radiation and the stage of canopy development. Diurnal variations in CO2 and H2O vapor fluxes revealed that the magnitude of the fluxes is large and the variation of the fluxes among fields was consistent throughout the season. Integration of the daily fluxes into seasonal totals showed large differences among crops and fields. Flux differences were the result of the effect of varying soil types on water-holding capacity. Seasonal integrated values were lower than estimates derived from biomass samples collected within the fields and the measurement of the C content of the biomass. Within-canopy recycling of soil CO2 may provide insight to this discrepancy. The techniques are available to quantify the CO2 and H2O vapor fluxes across different management systems and landscapes to help refine our understanding of the magnitude of the CO2 and H2O dynamics in cropping systems.