We investigated the effects of several environmental factors on eelgrass abundance before, during, and after widespread eelgrass diebacks during the unusually hot summer of 2005 in the Chesapeake Bay National Estuarine Research Reserve in Virginia. Systematic sampling with fixed transects was used to investigate changes in eelgrass abundance at downriver and upriver regions of the York River Estuary. Concurrently, continuous and discreet measurements of water quality were made at fixed stations in each area within the eelgrass beds from 2004 through 2006. Results indicate nearly complete eelgrass vegetative dieback during the July–August period of 2005, in contrast to the more seasonal and typical declines in the summer of 2004. Losses were greatest in the deeper areas of the beds and at the upriver site where light availabilities were lowest. Recovery of eelgrass during 2006 was greater in the downriver area, especially at mid-bed depths. By the fall of 2006, no shoot vegetation remained at the upriver site. In 2005, the frequency and duration of water temperatures exceeding 30°C were significantly greater than that of 2004 and 2006. Additionally, the frequencies of low dissolved oxygen excursions of 1–3 mg L−1 during this period were greater in 2005 than 2004 or 2006. These results suggest that eelgrass populations in this estuary are growing near their physiological tolerances. Therefore, the combined effects of short-term exposures to very high summer temperatures, compounded by reduced oxygen and light conditions, may lead to long-term declines of this species from this system.