The terrestrial ecosystem plays a vital role in regulating regional and global carbon budgets. Ecosystem models are extensively employed to estimate carbon fluxes across different spatial scales. However, there remains a need to reduce the uncertainties associated with model parameterization and input data. To address these limitations, we assessed a distributed-calibration and independent-verification (DCIV) approach that uses (1) remotely sensed net primary production (NPP) and evapotranspiration (ET) data from the Moderate Resolution Imaging Spectroradiometer (MODIS), (2) multi-site eddy covariance net ecosystem exchange (NEE) data; and (3) field sampling of soil organic carbon (SOC) and aboveground biomass (ABG) data to improve the overall predictability of carbon fluxes for the different land use and land cover (LULC) types at a watershed scale. The DCIV approach was applied to an advanced version of the Soil and Water Assessment Tool (SWAT)-Carbon (or SWAT-C), equipped with Century-based SOC algorithms to simulate carbon dynamics for watersheds with heterogeneous vegetation. The objective of the modeling effort was to assess carbon stocks and fluxes under different land management scenarios for a 3000-acre experimental farm and forest preserve in the northeastern United States. Our study showed that a large SOC stock of at least 100 tons ha−1 is stored under mixed forest, deciduous, shrubland, and floodplain (grass). Our study also showed that converting floodplain (grass) to deciduous forest has the potential to increase CO2 uptake (-NEE) by an order of three magnitude and ABG by 77 %, leading to an increased SOC stock of 23 % after twenty years. Similarly, we found that converting ungrazed grassland to grazed pasture leads to a non-statistically decreasing trend of SOC, especially in the 0–30 cm soil layer. Thus, the methodology used in this study can be applied to improve carbon dynamic prediction from a heterogeneous watershed at a regional scale.