The objective of this study is to examine interannual variability of carbon dioxide exchange and relevant controlling factors in irrigated and rainfed maize–soybean agroecosystems. The mean annual gross primary production (GPP) of irrigated and rainfed maize was 1796 ± 92 g C m−2 y−1 (±standard deviation) and 1536 ± 74 g C m−2 y−1, respectively. Mean annual GPP of soybean (average of irrigated and rainfed crops) was about 56% that of maize. Light use efficiency of maize and soybean during clear sky conditions were 1.96 ± 0.10 and 1.37 ± 0.06 g C MJ−1, respectively. A light use efficiency model, incorporating sensitivity to diffuse light, provided a reasonable simulation of daily GPP of maize and soybean (r2 = 0.89–0.98 and 0.85–0.97, respectively). Simulated growing season GPP totals were within about 10% of the measured values. The green leaf area index (LAI) played a dominant role in explaining interannual variability of GPP in maize. For soybean, both LAI and PAR contributed to the interannual variability. Mean growing season ecosystem respiration (Re) totals were 1029 ± 46 g C m−2 for irrigated maize and 872 ± 29 g C m−2 for rainfed maize. The growing season Re total of soybean (average of irrigated and rainfed crops) was about 78% that of maize. A relationship, based on a reference soil respiration (Re20), air temperature (Ta), and LAI, simulated daily growing season Re reasonably well for maize and soybean (r2 = 0.77–0.91 and 0.51–0.94, respectively). Modeled Re totals during the growing season were generally within 10% of the measured values. Variations in the LAI and Re20 explained the majority of the interannual variability in growing season Re for maize. In addition to LAI and Re20, Ta also contributed to the soybean Re variability. Non growing season Re contributed 10–20% and 17–24% of annual Re in maize and soybean, respectively and was primarily controlled by air temperature and residue biomass (r2 ∼ 81%). About 70% of maize GPP was lost in Re, resulting in the mean annual net ecosystem CO2 production (NEP) of 552 ± 73 g C m−2 y−1 for irrigated maize and 471 ± 52 g C m−2 y−1 for rainfed maize. For soybean, however, most of the annual GPP was lost in Re resulting in a mean annual NEP of −57 ± 43 and 10 ± 52 g C m−2 y−1 for irrigated and rainfed soybean, respectively. In general, as compared to Re, GPP contributed more to explaining the departures (ΔNEP) of NEP from the 4-year mean for maize. Both GPP and Re contributed to the ΔNEP for soybean. Results on the net biome production (NBP) indicated that the irrigated maize–soybean rotation was initially a moderate source of carbon; however, the system appears to be approaching near C neutral recently. The rainfed maize–soybean rotation is approximately C neutral