Interdependencies between water and energy resources are emerging as one of the core concerns of resource management. Integrating a successful transition to low-carbon transportation technologies together with effective water resource management requires an understanding of regionally appropriate water-energy nexus impacts. This thesis seeks to further the understanding of the water use impacts of transport energy supply chains. In the first chapter, the development of a new model that can be used to estimate crop-water balances and irrigation water use across large geographic scopes is described. The model developed here, CropWatR, can be used to estimate annual and seasonal water flows between the soil, crops (or other non-forested landscapes), and the atmosphere at a daily time-step, and includes irrigation scheduling. It is made available on github and written in the R open-source language, which will be useful to other researchers in the future. In chapter two, the CropWatR model is applied to outputs of an integrated agriculture-energy-economic model designed to offer insights into the potential greenhouse gas (GHG) emissions, fuel use, and economic impacts of biofuel production incentivized by selected policy instruments in the United States. The regional and national crop-water balances and potential trade-offs in water resource consumption and availability are compared across two biofuel policy scenarios, including the current federal legislation (the Renewable Fuels Standard), a hypothetical national extension of a policy similar to California's Low Carbon Fuel Standard (LCFS), and a no-policy counterfactual. Regional hotspots are identified where policies promoting domestic biofuels production might lead to decreased water resource availability. The third chapter focuses on the water use of all major energy supply chains providing energy for transport demand in California. The water use for in- and out-of-state oil and natural gas production, biofuel feedstocks cultivation, and electricity generation were characterized based on primary data sources within the state, and literature on the water footprint of energy production and transformation. This inventory of current water use intensity is combined with an energy-economic optimization model that projects energy pathways under various climate and energy policies (including California's 2050 GHG reduction target, Renewable Portfolio Standards, and the LCFS, inter alia) to project the water use implications of scenarios given California's climate, energy, and water policy. Chapters two and three provide case studies illustrating a lesson has been increasingly recognized in the literature and among policy makers: that effective resource management requires an integrated approach to understand the potential tradeoffs. Policy designs using integrated approach can maximize the benefits and can minimize unintended consequences.