Technical Abstract: The removal of corn stover or herbaceous crops such as switchgrass as feedstocks for bioenergy purposes has been shown to have significant benefits from energy and climate change perspectives. There is a potential, however, to adversely impact water and soil quality, especially in Midwestern USA states where the biomass feedstock production would predominantly occur. The overall goal of this research is to provide a thorough and mechanistic understanding of the relationship between stover and/or herbaceous crop production management practices and resulting range of impacts on soil and water quality, with a focus on eastern Iowa, USA. Comparisons of the production of these bioenergy crops to continuous corn and corn-soybean rotations on five different soils representative of the region were performed. The APEX model, which predicts crop yield and nutrient, carbon and soil flows within an integrated agricultural and hydrological system, provides a means to quantify sustainability metrics and is used to generate sufficient data to provide a greater understanding of the particular variables that affect water and soil quality than previously possible. Total nutrient losses to ground and surface water, total soil losses due to wind and water erosion, and cumulative soil carbon losses, all normalized to acreage and crop production are the metrics derived to rate sustainability. As anticipated, the results clearly show the superiority of herbaceous crop production from a soil and water quality perspective. They also show, however, that compared to traditional cropping systems (e.g., corn-soybean rotations with conventional tillage), soil and water quality degradation can be reduced (under certain soil types and no-till agricultural practices) at the same time stover is removed.