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Seagrass meadows are becoming increasingly stressed throughout the world, due to a variety of factors including anthropogenic nutrient and sediment loading, and extreme climatic events. Here we explore drivers of spatial and temporal community change over a 7-year period in the York River, Chesapeake Bay, VA. Historically, declines here in the dominant species, Zostera marina, have been related to a combination of short-term summertime heat stress events and chronically reduced water clarity. We quantified two temperature-driven Z. marina die-off events that resulted in a community switch from a slower growing, large climax species (Z. marina) to a faster growing, small pioneer species (Ruppia maritima) the following summer. Of the water quality variables studied here (water temperature, turbidity, and chlorophyll), water temperature was the only significant factor related to the monthly change in Z. marina cover. Our model did not find any significant drivers of change for R. maritima, though it appears to be more related to the abundance of Z. marina rather than changes to water quality. During die-off years, R. maritima is able to temporarily replace some of the lost Z. marina abundance by expanding its coverage in some areas of the bed, retreating again once Z. marina begins to recover. The extent of this replacement in terms of habitat quality is not well known and is an important area for future research, not just for seagrass beds, but for vegetated communities worldwide as their species composition is altered in response to climate change.