Sean McDonald maintains an active research program focused on marine ecology and natural resource issues, in which he focuses on applying ecological principles to problems involving exploitation, cultivation, and conservation of aquatic species in a changing global landscape. In particular, he is interested in responses to major agents of ecosystem change, such as climate change and invasive species, in human and natural systems.

Sean is also the Capstone instructor for the Program on the Environment. He directs the internship activities and senior interdisciplinary research of Environmental Studies students and assists them in developing an independent scholarly project that dovetails with their hands-on work.