Sustainability has recently emerged as a key issue in process systems engineering (PSE). Mathematical programming techniques such as mixed-integer programming and global optimization offer a general modeling framework for including environmental concerns in the synthesis and planning of chemical processes. Including environmental issues in the synthesis and planning of chemical processes poses significant challenges that have not yet been fully solved, and hence merit further attention. One major critical issue is how to systematize the search for alternatives leading to reductions in environmental impact. Furthermore, aside from anticipating the effect of uncertainties, which are quite pronounced in this area, there is the issue on how to cope with competing economic and environmental objectives. In the area of process synthesis we address the energy and water optimization of biofuel plants.  We present an optimization framework based on superstructure optimization that effectively accounts for energy and water integration, and illustrate its application to the optimization of corn-based ethanol and lignocellulosic bioethanol plants. In the area of supply chain optimization we consider first the design of an integrated supply chain for gasoline and ethanol that can deliver a variety of blends. We also address the environmentally conscious design and planning of hydrogen supply chains for vehicle use using a multiobjective optimization approach coupled with the Eco-indicator 99 to assess the effect on human health.