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Water consumption has become a serious concern in renewable fuels production. This paper proposes a framework to address sustainable transport systems design where both environmental (i.e. carbon and water footprints) and economic performances are taken into account along the bioethanol supply chain. A multi‐objective Mixed Integer Linear Programming modeling framework supporting strategic design and planning decisions for multi‐period and multi‐echelon upstream ethanol supply chains is developed. Hybrid biofuel production networks, where both corn grain and stover are used as suitable feedstocks, are optimized according to several features, involving technology selection and by‐products end‐use option. A case study is presented referring to the emerging Italian biofuels market. Results show the effectiveness of mathematical‐programming‐based tools to optimal design of biofuels supply …