Production of fuel ethanol in the United States has increased ten-fold since 1993, largely as a result of government programs motivated by goals to improve domestic energy security, economic development, and environmental impacts. Over the next decade, the growth of and eventually the total production of second generation cellulosic biofuels is projected to exceed first generation (e.g., corn-based) biofuels, which will require continued expansion of infrastructure for producing and distributing ethanol and perhaps other biofuels. In addition to identifying potential differences in tailpipe emissions from vehicles operating with ethanol-blended or ethanol-free gasoline, environmental comparison of ethanol to petroleum fuels requires a comprehensive accounting of life-cycle environmental effects. Hundreds of published studies evaluate the life-cycle emissions from biofuels and petroleum, but the operation and maintenance of storage, handling, and distribution infrastructure and equipment for fuels and fuel feedstocks had not been adequately addressed. Little attention has been paid to estimating and minimizing emissions from these complex systems, presumably because they are believed to contribute a small fraction of total emissions for petroleum and first generation biofuels. This research aims to quantify the environmental impacts associated with the major components of fuel distribution infrastructure, and the impacts that will be introduced by expanding the parallel infrastructure needed to accommodate more biofuels in our existing systems. First, the components used in handling, storing, and transporting feedstocks and fuels are physically characterized by typical operating throughput, utilization, and lifespan. US-specific life-cycle GHG emission and water withdrawal factors are developed for each major distribution chain activity by applying a hybrid life-cycle assessment methodology to the manufacturing, construction, maintenance and operation of each component. Emissions from activities at the end of life of equipment and infrastructure are not included, as these activities have previously been shown to contribute negligibly to life-cycle emissions. Life-cycle transportation mode GHG emission factors per tonne-kilometer (t-km) are presented for long distance pipelines (5-20 g CO2-e/t-km), ocean tankers (5-17 g/t-km), fuel-carrying barges (31 g/t-km), fuel-carrying unit trains (25 g/t-km), tanker trucks (140-180 g/t-km), and bale-transporting flatbed trucks (200 g/t-km). Life-cycle emission factors are also presented per tonne of material throughput for several types of agricultural equipment (600-19,000 g CO2-e/t handled), fuel conversion facilities (9,000-98,000 g/t), fuel storage and dispensing facilities (2,000-12,000 g/t), and the portion of passenger vehicle operations dedicated to refueling errands (2,000-200,000 g/t). The emissions intensity ranges reported for specific transportation modes are largely due to the greater energy efficiency of larger vehicles and pipelines, and the emissions intensity ranges within stationary storage and handling equipment is often due to differences in utilization of capital equipment and/or material losses during storage and handling activities. Consistent with existing literature, the contribution of non-operation stages to life-cycle GHG emissions ranges from 20% to 40% for most of the components modeled. Criteria air pollutant (NOx, PM2.5, SOx, VOC, CO) emission factors are also presented for the operation stage (e.g., tailpipe only) of each transportation mode. In order to apply the new emission factors to policy-relevant scenarios, a projection is made for the fleet inventory of infrastructure components necessary to distribute 21 billion gallons of ethanol (the 2022 federal mandate for advanced biofuels under the Energy Independence and Security Act of 2007) derived entirely from Miscanthus grass, for comparison to the baseline petroleum system. Due to geographic, physical and chemical properties of biomass and alcohols, the distribution system for Miscanthus-based ethanol is more capital- and energy-intensive than petroleum per unit of fuel energy delivered. Assuming steady-state annual turnover, operation, and maintenance of infrastructure to supply the projected quantities of ethanol and petroleum fuels, ethanol is estimated to be approximately five times more GHG and water intensive than petroleum (i.e., GHG emissions of more than 17 g CO2-e/MJ versus 3 g/MJ, and water withdrawals of 380 L/MJ vs. 77 L/MJ of consumed fuel, neglecting feedstock production and conversion). Embodied GHG emissions from manufacturing and maintaining infrastructure, equipment, and vehicles make up less than half of these emissions, at approximately 1 g CO2-e/MJ of petroleum fuel and 8 g CO2-e/MJ of ethanol. Although petroleum fuels are projected to supply twenty times the energy content of ethanol in 2022, the annual GHG and water withdrawal footprint of petroleum's liquid fuel infrastructure and distribution system is slightly less than four times that of ethanol (i.e., 110 vs. 30 million tonnes of CO2-e and 2,500 vs. 640 billion liters of water). Opportunities to significantly reduce emissions include shifting transportation to more efficient modes, consuming products closer to producers, and converting biorefineries to produce fuel with higher energy density than ethanol. Minimizing fuel transportation distance is believed to be the most feasible and cost-effective opportunity to reduce emissions in the near term. The transportation of biofuels away from producer regions poses environmental, health, and economic trade-offs that are herein evaluated using a simplified national distribution network model. In just the last ten years, ethanol transportation within the contiguous United States is estimated to have increased more than ten-fold in total t-km as ethanol has increasingly been transported away from Midwest producers due to air quality regulations pertaining to gasoline, renewable fuel mandates, and the 10% blending limit (i.e., the E10 blend wall). From 2004 to 2009, approximately 10 billion t-km of ethanol transportation are estimated to have taken place annually for reasons other than the E10 blend wall, leading to annual freight costs greater than $240 million and more than 300,000 tonnes of CO2-e emissions and significant emissions of criteria air pollutants from the combustion of more than 90 million liters of diesel. Although emissions from distribution activities are small when normalized to each unit of fuel, they are large in scale. Archetypal fuel distribution routes by rail and by truck are created to evaluate the significance of mode choice and route location on the severity of public health impacts from locomotive and truck emissions, by calculating the average PM2.5 pollution intake fraction along each route. Exposure to pollution resulting from trucking is found to be approximately twice as harmful as rail (while trucking is five times more energy intensive). Transporting fuel from the Midwest to California would result in slightly lower human health impacts than transportation to New Jersey, even though California is more than 50% farther from the Midwest than most coastal Northeast states. In summary, this dissertation integrated concepts from infrastructure management, climate and renewable fuel policy, fuel chemistry and combustion science, air pollution modeling, public health impact assessment, network optimization and geospatial analysis. In identifying and quantifying opportunities to minimize damage to the global climate and regional air quality from fuel distribution, results in this dissertation provide credence to the urgency of harmonizing policies and programs that address national and global energy and environmental goals. Under optimal future policy and economic conditions, infrastructure will be highly utilized and transportation minimized in order to reduce total economic, health, and environmental burdens associated with the entire supply and distribution chain for transportation fuels.