These files contain data and R code supporting all results reported in Graham et al. "Deeper habitats and cooler temperatures moderate a climate-driven disease in an essential marine habitat." In Graham et al., we found: Eelgrass creates critical coastal habitats worldwide and fulfills essential ecosystem functions as a foundation seagrass. Warming and disease threaten eelgrass meadows with mass mortalities and cascading ecological impacts, even in pristine locations. Although deeper, subtidal meadows are valuable fish nursery grounds and may also provide refuge from the climate-fueled seagrass wasting disease, nothing is known about differences in disease levels across remote locations in northern latitudes and between tidal zones (intertidal and subtidal meadows). From cross-boundary surveys on 5,761 eelgrass leaves from Alaska to Washington assisted with a machine-language algorithm, we measured outbreak conditions with average disease prevalence over 66% in intertidal and 50% in subtidal. In field surveys, disease was consistently lower in subtidal compared to adjacent intertidal meadows; remotely-sensed temperatures revealed significant associations between spring temperature anomalies and disease. While new studies show links between warm temperature anomalies and increased disease, our work detects beneficial effects of cooling in colder water anomalies. Disease was reduced in all regions except Puget Sound in the cooler summer of 2017. Pooled across both years, predicted disease prevalence was nearly 40% lower for subtidal than intertidal leaves, but in both tidal zones, disease risk was lower for plants in cooler conditions. Even in the ecologically most valuable subtidal meadows, we observed high disease levels, with half of the sites exceeding 50% prevalence. Disease models predicted reduced disease prevalence and severity under cooler conditions, confirming a strong interaction between disease and temperature. Finally, at both tidal zones, prevalence was reduced in more dense eelgrass meadows, suggesting disease is suppressed in healthy, higher density meadows. These results highlight the value of subtidal eelgrass meadows and meadows in cooler locations as refugia from the highest disease levels, indicate cooling can suppress disease, and have implications for eelgrass conservation and management under future climate change scenarios.