Texas High Plains (THP), which is an important cotton (Gossypium hirsutum L.) growing region in the United States faces challenges from declining/deteriorating groundwater levels/quality, recurring droughts and severe wind erosion. Growing cover crops after harvesting cotton and/or changing land use from cotton to perennial bioenergy crops could not only address above challenges, but also assist in meeting the national biofuel target. The objective of this study is to assess the implications of changes in land use (replacing cotton with Alamo switchgrass (Panicum virgatum L.) and Miscanthus x giganteus) and crop management (growing winter wheat (Triticum aestivum L.) cover crop) on hydrology and wind erosion in the Double Mountain Fork Brazos Watershed using the Agricultural Policy/Environmental eXtender (APEX) model. Simulated average annual wind erosion, total nitrogen (TN) loss to surface water and nitrate-nitrogen (NO3-N) leaching to groundwater reduced by more than 37%, 43% and 73%, respectively, when winter wheat was grown as a cover crop under the 457mm (18-inch) annual groundwater pumping limit setup by the High Plains Water District. In addition, winter wheat produced about 0.20-0.26 kgm(-2) of biomass for biofuel purposes. Land use change from irrigated cotton to switchgrass and rainfed cotton to Miscanthus decreased the TN load, NO3-N leaching and soil loss by wind erosion by > 89% relative to the baseline scenario. Under the groundwater pumping restrictions, multiple harvests of perennial grasses were found to be better in terms of biomass production (> 2 kgm(-2)), and protection of groundwater and soil.