While disease is a part of all natural systems, emerging marine diseases are on the rise and many are exacerbated by anthropogenic stressors. Marine and terrestrial environments are fundamentally different, requiring a suite of new approaches to understanding and managing the host–pathogen–environment relationship. Promising strategies include establishing marine protected areas, developing forecasting tools, and using natural ecosystem filters to control pathogens. Aquaculture is one measurable avenue by which natural systems come into direct contact with managed systems, often with negative consequences. This chapter presents examples where pathogens, invasive species, and degraded water quality are associated with impacts on adjacent natural systems. While effective regulatory procedures exist, international transport presents a challenge to implementation and needs special attention. Ecological restoration, a growing management science, would benefit from consideration of disease processes, such as genotyping to determine differences in natural resistance that could be used to guide selective breeding efforts.