Biofuels production has been promoted in the attempt to address global warming and oil dependence concerns. However, the environmental impact of biofuels is a very complex issue and cannot be represents by GHG (greenhouse gas) emissions only (carbon footprint). In particular, water consumption (water footprint) has been recognized as a key issue in renewable fuels production. This paper proposes a multiobjective Mixed Integer Liner Programming modeling framework to optimize the environmental (i.e., the carbon and water footprints) and economic performances of bioethanol supply chains. Multiechelon, multiperiod, and spatially explicit features are embedded within the formulation to steer decisions and investments through a global approach. The strategic design and planning of corn- and stover-based bioethanol production networks is taken into account. A case study is presented referring to the emerging Italian ethanol production. Results show the effectiveness of mathematical programming-based tools to provide decision makers with a quantitative analysis assessing the economic and environmental performances of different design configurations.