As we increase our studies of marine diseases and their population- and community- level impacts, the role of opportunist pathogens in causing disease is often overlooked. These pathogens are often ubiquitous in the environment, but cause disease only under certain conditions such as immunosuppression due to environmental stress. While direct management of pathogens is often unrealistic in the marine environment, management of the environmental stressors leading to increased vulnerability to disease may be possible. Eelgrass wasting disease, caused by the opportunist pathogen, Labyrinthula zosterae, is commonly associated with severe population declines of the temperate seagrass Zostera marina at times resulting in a local extinction event. While this pathogen is omnipresent, disease outbreaks only occur occasionally. Factors that lead to these outbreaks are largely unknown, however some phenolic compounds have been shown to inhibit L. zosterae in vitro. It has been hypothesized that environmental stressors causing decreased phenolic concentrations will cause more disease. Here we present survey data of a current outbreak of eelgrass wasting disease in the San Juan Archipelago and Northern Puget Sound regions of the Salish Sea. We confirm that lesions in the field are due to infection with Labyrinthula using histology and culturing techniques. Then we describe the relationship between climatic factors including water movement and temperature, host factors including demography and phenolic concentrations and disease prevalence across 11 sites. At some of these sites eelgrass standing stock is in decline. We discuss the relevance of our work to seagrass declines in the Salish Sea and regional practices designed to protect Z. marina.