The use of bio-based fuels for energy generation can have positive or negative impacts on water and resources. To best understand these impacts, the effects of bioenergy systems on water and soil resources should be assessed as part of an integrated analysis considering environmental, social and economic dimensions. Bioenergy production systems that are strategically integrated in the landscape to address soil and water problems should be promoted where their establishment does not cause other negative impacts that outweigh these benefits. While standardized metrics, such as footprints and waterand nutrient-use efficiencies are convenient and intuitive, these factors can be insufficient to achieving sustainable production and environmental security at relevant spatial and temporal scales. Comprehensive ecosystem impact analysis should be conducted to ensure that sustainability standards like water quality, water supply, and soil integrity are consistent with other agricultural and silvicultural sustainability goals at the local, regional, and global level.