Dan Reed's primary research interests pertain to the ecology on coastal marine ecosystems and the ecological and physical processes that structure them. Much of his work has focused on determining the mechanisms that allow these systems to recover from natural disturbance and the application of this knowledge to restoration programs designed to mitigate impacts caused by human disturbance. Giant kelp forests and seagrass beds have been the focal ecosystems for most of his research, which includes studies on dispersal, recruitment, reproduction, population dynamics, community ecology, primary production and trophic interactions.