Boesch is a biological oceanographer who has conducted research in coastal and continental shelf environments along the Atlantic Coast and in the Gulf of Mexico, eastern Australia and the East China Sea. He has published two books and more than 90 papers on marine benthos, estuaries, wetlands, continental shelves, oil pollution, nutrient over-enrichment, environmental assessment and monitoring and science policy. Presently, his research focuses on the use of science in ecosystem management.

His dissertation research and much of his earlier research focused on the ecology of benthic communities in estuarine and continental shelf environments. This work addressed distribution patterns in relationship to environmental factors (involving extensive application of multivariate statistics), diversity and community structure, benthic communities as indicators of environmental health, the effects of organisms on sediment structure, and predation by bottom-feeding fishes and invertebrates. 

While serving as executive director of the Louisiana Universities Marine Consortium, he initiated or participated in research programs on: processes affecting coastal wetland loss, the causes and consequences of the oxygen depletion of bottom waters on the continental shelf, and the effects of discharges (particularly produced waters) from oil and gas production facilities. 

Since joining the faculty of the University of Maryland Center for Environmental Science, his research activities have become exclusively synthetic. He has been performing research and writing on the use of science in environmental policy and management, particularly related to understanding the causes of and solutions to coastal eutrophication, and on the impacts of global climate change.