The tighter linkages between energy and crop markets due to recent climate and energy legislation in the US have large potential environmental impacts beyond carbon sequestration and climate mitigation. These range from effects on water quality and quantity, soil erosion, habitat and biodiversity preservation. These impacts are very location and management-decision specific, as they are the product of atomistic decisions and depend on soil and landscape specific variables. In order to fully understand the effects of biomass markets, the new and stronger linkages and feedback effects between national- and global-scale energy and commodity markets must be properly understood and identified using an integrated perspective. We discuss the various interactions between agricultural and energy markets and their environmental impacts for existing biomass crops and detail how these interactions may be strengthened with the emergence of corn stover as a second generation biofuel feedstock. The tighter coupling of land use and management and energy systems needs to be accounted for to ensure that we have accurate indicators of the sustainability of biomass as an energy resource.