Climate change has emerged as one of the most problematic issues and key global threats to mankind, and sustainability has become an important issue for any organizations. Therefore, managing supply chains in a more sustainable way has become an increasing concern for many businesses across a wide range of companies around the world. Designing efficient and effective supply chains improves overall environmental performance in business operations and is essential to not only mitigate climate change, but also to benefit human life and environment. The objective of this dissertation is to address issues in sustainability of transportation and supply chains with three essays focusing on three aspects - measure, manage, and mitigate - that contribute to the practice and literature of sustainable transportation and supply chain. Chapter Two of this dissertation utilizes slack-based date envelopment analysis to form an environmental efficiency index comprising various sustainability indicators in transportation sector. This index may function as a decision-making tool for transportation planners and practitioners to compare sustainability performance of U.S. states, to benchmark sustainability performance, and also to develop carbon emission reduction strategies. Chapter Three of this dissertation adopts multimodal transportation to formulate the cost-effective strategies for managing a switchgrass-based biofuel supply chain. This study captures the benefit of a modal shift in designing the biofuel supply chain network; thus, practitioners who want to plan for multimodal transportation of biofuel can learn its practical relevance. Chapter Four of this dissertation address greening the biomass supply chain for animal manure by formulating mathematical model for design and management of biomass to a biogas supply chain, including anaerobic digestion as a source of renewable energy production. This study handled waste management issues by incorporating carbon policy into the biomass supply chain, with due consideration accorded to both monetary and environmental factors. Overall, the research outcome will provide practitioners and researchers with scientific information and tools that will enable them to become better stewards by virtue of healthy and sustainable development and practices in transportation and supply chain.