The main laboratories and offices of SoMAS are housed in a cluster of buildings on South Campus with more than 8,000 square meters of usable floor space. Laboratories are well equipped for most analyses, and students and faculty have access, with special arrangements, to nearby Brookhaven National Laboratory (BNL) and Cold Spring Harbor Laboratory. In addition to ITPA, SoMAS is home to the Institute for Ocean Conservation Sciences, the Marine Animal Disease Laboratory, a diagnostic and research facility focused on the health of living marine resources, the Waste Reduction and Management Institute, the Living Marine Resources Institute, the Long Island Groundwater Institute, the New York Sea Grant College Program, and several analytical facilities. The Safina Institute also maintains an office at SoMAS. The Marine and Atmospheric Sciences and Information Center (MASIC) is the branch of the campus library system located at SoMAS. Officially designated as a prototype for technology-based branch libraries on the campus, MASIC offers students and faculty a core collection of journals and monographs relevant to the multi-disciplinary pursuits of SoMAS and its affiliated institutes as well as a state-of-the-art computer teaching laboratory.

SoMAS manages the Flax Pond Marine Laboratory located on a 0.6 square kilometer salt marsh approximately seven kilometers from campus. This facility provides flow-through seawater and space suitable for culture and experimentation on living marine resources. Part of the facility is in a green house offering ambient light and temperature conditions.   Laboratory and sea-table space are available to faculty and students at SoMAS and other collaborating university programs. SoMAS also manages the newly renovated marine station at Stony Brook Southampton, located 46 miles away on the beautiful east end of Long Island. State of the art class rooms, laboratories and animal culture facilities are available in the new Southampton Marine Station. Several SoMAS faculty keep research laboratories at Stony Brook Southampton, and additional wet lab space is available in the new Marine Station for student and faculty research.

SoMAS operates a fleet of research vessels, the largest of which is the R/V SEAWOLF, a 24-meter research vessel designed specifically for oceanographic research. The SEAWOLF is ideally suited for extended research trips, large-scale oceanographic sampling, and trawling. Several other smaller boats are available for local cruises out of either the Stony Brook or Southampton campuses.