The bioenergy mandate under Energy Independence and Security Act (EISA 2007) will result in large scale land-use changes in the US if it is ever fully realized. Energy crops such as switchgrass (Panicum virgatum) and miscanthus (Miscanthus X giganteus) can grow well throughout the continental United States; however, most studies on the water quality impacts of land-use change from bioenergy policy are based in the Midwest. Insufficient research has been conducted to determine whether the results from the Midwest are applicable to other regions in the United States. This study compares water quality impacts of converting from corn to switchgrass in the Midwest (Upper Cedar watershed) and Southeast (Lumber watershed) with nitrogen loading to surface water as a proxy metric for overall water quality impacts using the Soil and Water Assessment Tool (SWAT). The analysis shows that the fraction of nitrogen runoff compared to the fertilizer applied is 36% in Upper Cedar as compared to 6% in Lumber. Existing management practices like tile-drainage and land-cover like riparian wetlands contribute to this difference in the baseline nitrate export from each watershed. The potential reduction in nitrogen loading per potential liter of ethanol to surface waters, which account for both nitrate export and productivities, from the baseline corn-soy to switchgrass is about 40% for the Upper Cedar watershed and around 80% for the Lumber watershed. Although, the trend in reduction is similar in both watersheds, this study shows that results extrapolated from the Midwest may not be representative of other bioenergy producing regions. (C) 2017 Elsevier Ltd. All rights reserved.