Reducing dependence on fossil-based energy has raised interest in biofuels as a potential energy source, but concerns have been raised about potential implications for water quality. These effects may vary regionally depending on the biomass feedstocks and changes in land management. Here, we focused on the Tennessee River Basin (TRB), USA. According to the recent 2016 Billion-Ton Report (BT16) by the US Department of Energy, under two future scenarios (base-case and high-yield), three perennial feedstocks show high potential for growing profitably in the TRB: switchgrass (Panicum virgatum), miscanthus (Miscanthus × giganteus), and willow (Salix spp.). We used the Soil & Water Assessment Tool (SWAT) to compare hydrology and water quality for a current landscape with those simulated for two future BT16 landscapes. We combined publicly available temporal and geospatial datasets with local land and water management information to realistically represent physical characteristics of the watershed. We developed a new autocalibration tool (SWATopt) to calibrate and evaluate SWAT in the TRB with reservoir operations, including comparison against synthetic and intermediate response variables derived from gage measurements. Our spatiotemporal evaluation enables to more realistically simulate the current situation, which gives us more confidence to project the effects of land-use changes on water quality. Under both future BT16 scenarios, simulated nitrate and total nitrogen loadings and concentrations were greatly reduced relative to the current landscape, whereas runoff, sediment, and phosphorus showed only small changes. Difference between simulated water results for the two future scenarios was small. The influence of biomass production on water quantity and quality depended on the crop, area planted, and management practices, as well as on site-specific characteristics. These results offer hope that bioenergy production in the TRB could help to protect the region's rivers from nitrogen pollution by providing a market for perennial crops with low nutrient input requirements.