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Climate change is altering the distribution of marine species around the globe, including those providing critical 3-dimensional structure in important coastal habitats. We analysed how continued warming over the 21st century would affect the distribution of eelgrass Zostera marina, the dominant seagrass in the Northwest Atlantic and provider of essential ecosystem functions and services. We compiled presence-only occurrence records and built a species distribution model using Maxent to determine a present-day distribution, which was compared to physiological thresholds for eelgrass growth and reproduction. Present-day models were then projected to mid- (2040-2050) and end-century (2090-2100) using 2 contrasting emissions scenarios and different global climate models. Our projections suggest an average shift of the southern range limit by 1.41 degrees N to the north under a strong mitigation scenario (RCP 2.6) and 6.48 degrees N under a business-as-usual emissions scenario (RCP 8.5) by 2100, resulting in substantial loss of eelgrass habitat along the eastern coast of the USA. The northern edge shift was less certain, yet resulted in an expansion of total eelgrass habitat. To minimize the extent of eelgrass bed extinction and areas of reduced growth along the southern range, strong climate mitigation is critical. Moreover, warm-temperature stress in reduced-growth areas will greatly increase the susceptibility of eelgrass to other natural or anthropogenic stressors. Our results can inform coastal management and conservation planning to protect the essential structure, functions and services provided by eelgrass in a warming climate.