Large-scale bioenergy production will affect the hydrologic cycle in multiple ways, including changes in canopy interception, evapotranspiration, infiltration, and the quantity and quality of surface runoff and groundwater recharge. As such, the water footprints of bioenergy sources vary significantly by type of feedstock, soil characteristics, cultivation practices, and hydro-climatic regime. Furthermore, water management implications of bioenergy production depend on existing land use, relative water availability, and competing water uses at a watershed scale. This paper reviews previous research on the water resource impacts of bioenergy production-from plot-scale hydrologic and nutrient cycling impacts to watershed and regional scale hydro-economic systems relationships. Primary gaps in knowledge that hinder policy development for integrated management of water-bioenergy systems are highlighted. Four case studies in the Americas are analyzed to illustrate relevant spatial and temporal scales for impact assessment, along with unique aspects of biofuel production compared to other agroforestry systems, such as energy-related conflicts and tradeoffs. Based on the case studies, the potential benefits of integrated resource management are assessed, as is the need for further case-specific research.