Climate change is a global phenomenon that exerts significant impacts on ecosystems. Estuaries, as critical aquatic habitats, are susceptible to these changes; however, our comprehension of their specific responses to climate change remains limited. Beyond temperature rise and alterations in precipitation patterns, climate change induces indirect effects, influencing a multitude of biotic and abiotic variables within aquatic ecosystems. In this study, we assess seagrass health as an indicator of estuary well-being in three estuaries located in northern to central California, USA. Our investigation focuses on the marine angiosperm Zostera marina (commonly known as eelgrass) and its associated parasite, Labyrinthula zosterae. Z. marina, a temperate marine plant, faces the threat of eelgrass wasting disease (EWD) caused by the protist L. zosterae. Notably, this pathogen demonstrates sensitivity to warming ocean temperatures, underscoring the imperative to comprehend its impacts on host health amidst climate change. Our study assessed EWD prevalence with relation to spatial and temporal patterns, the relationship, if any, between disease prevalence and eelgrass percent cover, the spatial patterns, if any, of eelgrass percent cover, and what climatic variables were most strongly correlated with EWD and eelgrass percent cover.