These files contain data and code supporting all results reported in Graham et al. "Data and scripts from: Deeper eelgrass are refugia from disease and environmental stressors." In Graham et al., we found: Eelgrass (Zostera marina) creates valuable, biodiverse habitats worldwide, but is at risk from combined environmental stressors and disease. We surveyed paired intertidal and subtidal meadows for seagrass wasting disease in the San Juan Islands, WA, USA in summers 2017-2019 to determine how disease varied with depth, salinity and temperature, and the influence of eelgrass densities on disease. We anticipated reduced disease in deeper meadows with narrower temperature and salinity ranges (i.e. more stable environments) compared to shallower, intertidal meadows, and reduced densities in meadows with high disease. Leveraging a machine-learning algorithm for detection and quantification of disease, we detected high levels of disease and large changes in meadow densities, particularly in the warmer 2018 summer. Daily mean in situ and remote-sensed temperatures captured exposure to warming, though in situ temperatures better identified site-specific, seasonal thermal ranges. Subtidal meadows experienced nearly 14°C cooler maximum in situ temperatures compared to intertidal meadows. Disease severity was significantly reduced by 8.34 ± 0.012% in deeper, subtidal meadows compared to shallower, intertidal over the entire study and by 11.88 ± 0.13% (mean ± SE) during the 2018 warming, indicating that subtidal meadows may serve as valuable refugia against environmental and pathogenic stressors. Reduced eelgrass densities were also associated with increased severity, suggesting an important link between disease and meadow size. Disease prevalence was also associated with greater salinity ranges, emphasizing salinity as a key factor in eelgrass health. Our work highlights the strong value of both subtidal meadows and sites with more stable environmental conditions as refugia from multiple stressors. More broadly, understanding how eelgrass responds to various stressors can directly inform conservation and management efforts within and beyond the Salish Sea.