SignificanceClimate change creates ecosystems with fundamentally different conditions and species than in the past. In the Chesapeake Bay, rising temperatures have interacted with nutrient pollution to halve the cover of the historically abundant but climate change-vulnerable seagrass, eelgrass. In contrast, the heat-tolerant and opportunistic seagrass, widgeongrass, has nearly doubled in extent. Widgeongrass’ rapid recolonization ability has fueled the two largest recorded increases in the Chesapeake Bay seagrasses since 1984, but also a devastating die-back in 2019. Shifting species dominance has created an ecosystem that is stochastic but also is influenced more by regional nutrient management than global climate change, leading to new opportunities and challenges to maintain healthy and viable coastlines.