Carbon dioxide exchange was quantified in maize–soybean agroecosystems employing year-round tower eddy covariance flux systems and measurements of soil C stocks, CO2fluxes from the soil surface, plant biomass, and litter decomposition. Measurements were made in three cropping systems: (a) irrigated continuous maize, (b) irrigated maize–soybean rotation, and (c) rainfed maize–soybean rotation during 2001–2004. Because of a variable cropping history, all three sites were uniformly tilled by disking prior to initiation of the study. Since then, all sites are under no-till, and crop and soil management follow best management practices prescribed for production-scale systems. Cumulative daily gain of C by the crops (from planting to physiological maturity), determined from the measured eddy covariance CO2 fluxes and estimated heterotrophic respiration, compared well with the measured total above and belowground biomass. Two contrasting features of maize and soybean CO2 exchange are notable. The value of integrated GPP (gross primary productivity) for both irrigated and rainfed maize over the growing season was substantially larger (ca. 2:1 ratio) than that for soybean. Also, soybean lost a larger portion (0.80–0.85) of GPP as ecosystem respiration (due, in part, to the large amount of maize residue from the previous year), as compared to maize (0.55–0.65). Therefore, the seasonally integrated NEP (net ecosystem production) in maize was larger by a 4:1 ratio (approximately), as compared to soybean. Enhanced soil moisture conditions in the irrigated maize and soybean fields caused an increase in ecosystem respiration, thus eliminating any advantage of increased GPP and giving about the same values for the growing season NEP as the rainfed fields. On an annual basis, the NEP of irrigated continuous maize was 517, 424, and 381 g C m−2 year−1, respectively, during the 3 years of our study. In rainfed maize the annual NEP was 510 and 397 g C m−2 year−1 in years 1 and 3, respectively. The annual NEP in the irrigated and rainfed soybean fields were in the range of −18 to −48 g C m−2. Accounting for the grain C removed during harvest and the CO2 released from irrigation water, our tower eddy covariance flux data over the first 3 years suggest that, at this time: (a) the rainfed maize–soybean rotation system is C neutral, (b) the irrigated continuous maize is nearly C neutral or a slight source of C, and (c) the irrigated maize–soybean rotation is a moderate source of C. Direct measurement of soil C stocks could not detect a statistically significant change in soil organic carbon during the first 3 years of no-till farming in these three cropping systems.