The SoMAS Southampton Marine Station is located on Old Fort Pond in Shinnecock Bay, a short walk from the main campus. From the facility, students and faculty have direct access to local bays, estuaries, and the Atlantic Ocean. The marine station is the site of five laboratories and a fleet of boats including the R/V Paumanok, a 44-foot ocean-going vessel used for coastal research, the R/V Shinnecock, a 35-foot platform craft used for sampling local bays and estuaries and the R/V Peconic, a 45-foot catamaran, houseboat-style vessel for operation in protected bays and rivers. Smaller outboard craft are equipped with winches, davits and metering wheels for sampling instruments such as oxygen analyzers, CTD-probes, and trawls. The aquarium/wet laboratory allows maintenance of live marine species throughout the year for classroom use.

A three-laboratory facility was completed in early 1986 to complement the existing structures. These laboratories house standard equipment including an autoanalyser, atomic absorption spectrophotometer, salinometer, fluorimeter, osmometer, and Coulter Counter. Faculty utilize these facilities for their research, and students are encouraged to utilize these facilities and instruments during their course work and while undertaking independent studies.

Current weather station readings at the Stony Brook Southampton Marine Station.