This dataset contains daily estimates of carbon fluxes in croplands derived from the "ecosys" model covering a portion of the Midwestern US (Illinois, Indiana, and Iowa) at county-level resolution from 2001-2018. Ecosys simulates water, energy, carbon, and nutrient cycles simultaneously for various ecosystems, including agricultural systems at up to hourly resolution. Estimates include: gross primary productivity (GPP), net primary productivity (NPP), autotrophic respiration (Ra), heterotrophic respiration (Rh), or net ecosystem exchange (NEE). Data were generated by the ecosys model constrained by observational data, including USDA crop yield from USDA National Agricultural Statistics Service, and a remote-sensing-based SLOPE GPP product. Model performance was evaluated using observations from AmeriFlux towers at agricultural sites within the study area. Agriculture in the US Midwest produces significant quantities of corn and soybeans, which are key elements to the global food supply. The data are provided in shapefile format.