Bioenergy crop production has the potential to protect marginal crop lands that generate high surface runoff and produce poor crop yields. Long-term evaluation of the impacts of such land use change on hydrologic fluxes and biofuel production potential is necessary before adopting such strategies on a large scale. In this study, the hydrologic impacts of replacing cotton (Gossypium hirsutum L.) on marginal lands in an intensive agricultural watershed in the Texas High Plains with Alamo switchgrass (Panicum virgatum L.) as a bioenergy crop were evaluated using the Agricultural Policy/ Environmental eXtender (APEX) model. The surface runoff to cotton yield ratio was used as a criterion to identify marginal cotton subareas (homogenous spatial units delineated by APEX) in the study watershed, and three replacement scenarios (low (9 %), medium (33 %), and high (57 %) extents of cotton acreage replaced by switchgrass) were implemented in the scenario analysis. The average (1994)(1995)(1996)(1997)(1998)(1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)) annual surface runoff decreased by about 84 and 66 %, and the percolation increased by 106 and 57 % in the irrigated and dryland subareas, respectively, when cotton was replaced by switchgrass under the high replacement scenario. Spatial analysis showed that switchgrass was a feasible bioenergy crop for replacing cotton, especially in the western part of the study watershed, due to its higher water use efficiency and better water conservation effects compared to cotton. It is estimated that 193 and 381 million liters of ethanol could be produced from the dryland and irrigated subareas of the study watershed, respectively, under the high replacement scenario.