Carbon fluxes from agroecosystems contribute to the variability in the carbon cycle and atmospheric [CO₂]. In this study, we used the Integrated Science Assessment Model (ISAM) equipped with a spring wheat module to study carbon fluxes and their variability in spring wheat agroecosystems of India. First, ISAM was run in the site-scale mode to simulate the Gross Primary Production (GPP), Total Ecosystem Respiration (TER), and Net Ecosystem Production (NEP) over an experimental spring wheat site in the north India. Comparison with flux-tower observations showed that the spring wheat module in ISAM can match the observed flux patterns better than generic crop models. Next, regional-scale runs were conducted to simulate carbon fluxes across the country for the 1980-2016 period. Results showed that the fluxes vary widely, primarily due to variations in planting dates across regions. Fluxes peak earlier in the eastern and central parts of the country, where the crops are planted earlier. All fluxes show statistically significant increasing trends (p<.01) during the study period. The GPP, Net Primary Production (NPP), Autotrophic respiration (Ra), and Heterotrophic Respiration (Rh) increased at 1.272, 0.945, 0.579, 0.328, and 0.366 TgC/yr², respectively. Numerical experiments were conducted to study how natural forcings like changing temperature and [CO₂] and agricultural management practices like nitrogen fertilization and water availability could contribute to the increasing trends. The experiments revealed that increasing [CO2], nitrogen fertilization, and water added through irrigation contributed to the increase of carbon fluxes, with nitrogen fertilization having the strongest effect.