Temporal and spatial changes of soil organic C in terrestrial ecosystems are largely determined by a) the balance between C captured by photosynthesis and that released by respiration and b) the transfer of C inside and outside the ecosystem boundaries in harvested products, organic amendments and transport and deposition of soil particles by wind and water. A better understanding of the C balance at the landscape scale is required in order to make improved predictions of soil C sequestration at regional scales. Here we discuss and demonstrate the Agricultural Policy Environmental Extender (APEX), a watershed model based on a proven agroecosystem model (EPIC) but with the ability to model routing of water sediment and nutrients across fields under various management practices. We tested APEX for an area in Frederick County, MD using remote sensing and soil survey information to define the landscape. APEX routed the water, sediment and nutrients through the farm field, and the erosion and deposition of sediment and organic carbon was observed. The initial results demonstrate the ability of APEX to simulate soil C dynamics within the soil profile and across the landscape, thus providing a more complete view of the C balance in agroecosystems. In future studies, we will test the performance of APEX against experimental data.