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This paper presents a life-cycle emissions analysis of conventional and natural gas-based marine transportation in the United States. We apply a total fuel cycleor well-to-propelleranalysis that evaluates emissions along the fuel production and delivery pathway, including feedstock extraction, processing, distribution, and use. We compare emissions profiles for methanol, liquefied natural gas, and low sulfur marine fuel in our analysis, with a focus on exploring tradeoffs across the following pollutants: greenhouse gases, particulate matter, sulfur oxides, and nitrogen oxides. For our greenhouse gas analysis, we apply global warming potentials that consider both near-term (20-year) and long-term (100-year) climate forcing impacts. We also conduct uncertainty analysis to evaluate the impacts of methane leakage within the natural gas recovery, processing, and distribution stages of its fuel cycle. Our results indicate that natural-gas based marine fuels can provide significant local environmental benefits compared to distillate fuel; however, these benefits come with a near-termand possibly long-termglobal warming penalty, unless such natural gas-based fuels are derived from renewable feedstock, such as biomass. These results point to the importance of controlling for methane leaks along the natural gas production process and the important role that renewable natural gas can play in the shipping sector. Decision-makers can use these results to inform decisions related to increasing the use of alternative fuels in short sea and coast-wise marine transportation systems.