Land use change resulting from bioenergy production has the potential to affect regional water quality. Water quality impacts associated with bioenergy production have been extensively modeled in the Midwest, but are not sufficiently quantified for other regions. The Black Creek watershed is located in the Pee Dee River basin in South Carolina, an area that has high bioenergy production potential. Total nitrate loss from simulated switchgrass cultivation within the Black Creek watershed was modeled and compared with cotton, a major crop in the region. The Soil and Water Assessment Tool (SWAT) was used to simulate land use conversion from cotton to switchgrass during the establishment phase and matured phase of the perennial grass species. Management practices for both switchgrass and cotton were determined from experimental plots at the Clemson University Pee Dee Research and Educational Center at Florence, South Carolina. The study suggested that in the early years of growth there is significant nitrogen loss from switchgrass, which is greatly reduced as the switchgrass matures. The simulations suggested that during the establishment phase, the nitrogen loss from switchgrass was comparable to that of cotton and highly dependent upon the nitrogen fertilization rate. Over a fifteen-year period, the long-term loss of nitrogen from switchgrass in one-cut and two-cut systems was approximately 73% and 80% lower than nitrogen loss from cotton. (C) 2014 Elsevier Ltd. All rights reserved.