The small number of carbon dioxide (CO2) observation networks and the prohibitively high equipment cost restrict the estimation of net ecosystem CO2 exchange (NEE). Satellite-based remote sensing techniques have made it possible to obtain NEE and component carbon (C) fluxes. One-third of the world's cotton area is in India, but the information on NEE is limited. We used the Level 4 Carbon (L4_C) product from the Soil Moisture Active Passive (SMAP) mission to estimate C fluxes based on satellite-derived soil moisture, weather, and vegetation data. For our study (2018-19 to 2020-21), we chose two ecosystems (rainfed central India vs. irrigated northern India). Seasonal variations were observed in C fluxes. Gross primary productivity was the highest during the boll formation phase. This phase was the strongest sink and coincided with the highest CO2 uptake, followed by the flowering and square formation phases. The cotton crop was a C source during the initial vegetative phase and after the boll opening. Overall, the cotton crop was a sink for atmospheric CO2 with an average NEE value of −189.6 g C m−2 under irrigated and −245.6 g C m−2 in rainfed cotton. Higher ecosystem respiration in irrigated cotton resulted in lower C sink strength than rainfed cotton. Our studies indicate that the SMAP L4_C product model estimates can be used to obtain information on C fluxes in real-world situations. Moreover, such satellite-based remote sensing techniques will enable large-scale environmental monitoring with different cropping systems and support policymaking.