During the 21st century three components of climate change will impact Chesapeake Bay submerged aquatic vegetation (SAV) directly: increasing temperatures, coastal zone acidification, and sea level rise. Current understanding of these stressors, coupled with regional climate forecasts, permits us to make basic predictions for the future of SAV in the Chesapeake Bay. Summer heat waves have been linked to die-offs of SAV, especially eelgrass (Zostera marina) in the lower Bay. Thus, future climate warming is likely to have negative impacts on SAV populations already struggling with poor water quality/light limitation in the Chesapeake Bay. If the current trajectory of climate change continues the Chesapeake Bay could develop some characteristics of a subtropical estuary by the next century. Predicted warming has the potential to eliminate populations of temperate eelgrass (Zostera marina), favoring native heat-tolerant species such as widgeon grass (Ruppia maritima). A variety of subtropical plants and animals are likely to become more common in the region; however colonization by tropical seagrasses is unlikely in the near future due to continued low winter temperatures and winter ice. The “CO2 fertilization effect” of coastal acidification has the potential to stimulate photosynthesis and growth in at least some species of SAV. This may offset some of the deleterious effects of thermal stress. This may facilitate the survival of eelgrass in regions of the Chesapeake Bay. Sea level rise will reshape our shorelines. Where they are permitted to migrate landward, suitable SAV habitat may persist. However, where shorelines are hardened suitable SAV habitat is likely to be lost. The predictions are limited by a poor understanding of the indirect effects of climate change on organisms associated with seagrass die-offs, including fouling organisms, grazers, and microbes. These indirect effects may be powerful and may trigger abrupt, unforeseen changes in SAV communities.