The global increase in food demand in the context of climate change requires a clear understanding of cropland function and of its impact on biogeochemical cycles. However, although gas exchange between croplands and the atmosphere is measurable in the field, it is difficult to quantify at the plot scale over relatively large areas because of the heterogeneous character of landscapes and differences in crop management. However, assessing accurate carbon and water budgets over croplands is essential to promote sustainable agronomic practices and reduce the water demand and the climatic impacts of croplands while maintaining sufficient yields. From this perspective, we developed a crop model, SAFYE-CO₂, that assimilates high spatial- and temporal-resolution (HSTR) remote sensing products to estimate daily crop biomass, water and CO₂ fluxes, annual yields, and carbon budgets at the parcel level over large areas. This modeling approach was evaluated for sunflower against two in situ datasets. First, the model’s output was compared to data acquired during two cropping seasons at the Auradé integrated carbon observation system (ICOS) instrumented site in southwestern France. The model accurately simulated the daily net CO₂ flux (root mean square error (RMSE) = 0.97 gC·m⁻²·d⁻¹ and determination coefficient (R²) = 0.83) and water flux (RMSE = 0.68 mm·d⁻¹ and R² = 0.79). The model’s performance was then evaluated against biomass and yield data collected from 80 plots located in southwestern France. The model was able to satisfactorily estimate biomass dynamics and yield (RMSE = 66 and 54 g·m⁻², respectively). To investigate the potential application of the proposed approach at a large scale, given that soil properties are important factors affecting the model, a sensitivity analysis of two existing soil products (GlobalSoilMap and SoilGrids) was carried out. Our results show that these products are not sufficiently accurate for inclusion as inputs to the model, which requires more accurate information on soil water retention capacity to assess water fluxes. Additionally, we argue that no water stress should be considered in the crop growth computation since this stress is already present because of remote sensing information in the proposed approach. This study should be considered a first step to fulfill the existing gap in quantifying carbon budgets at the plot scale over large areas and to accurately estimate the effects of management practices, such as the use of cover crops or specific crop rotations on cropland C and water budgets.

To meet the incoming growth of the world’s food needs, and the demands of climate change, the agricultural sector will be forced to adapt its practices. To do so, the contribution of agricultural fields to greenhouse gas emissions, as well as the impact—on soil, climate and productions—of certain agricultural practices have to be known. In this study, the SAFY-CO₂ crop model is driven by remote sensing products in order to estimate CO₂ fluxes on the main crop rotation observed in the study area, i.e., winter wheat followed by sunflower. Different modeling scenarios are tested, particularly for intercropping periods, the approach being validated locally, thanks to eddy covariance flux measurements, and then applied regionally. Results showed that the model was able to reproduce crop production with high accuracy (rRMSE of 21% and 24% for winter wheat and sunflower yield, respectively) as well as daily net CO₂ flux (RMSE of 1.29 and 0.97 gC.m⁻².d⁻¹ for winter wheat and sunflower respectively). Moreover, the tested modeling scenarios highlight the importance of taking the regrowth events into account for assessing accurate carbon budgets. In a perspective of large-scale application, the model was upscaled over more than 100 plots, allowing discussion of the effect of regrowth on carbon uptake.