The Shannon Point Marine Center consists of state-of-the art educational and research facilities located on a forested 87 acre biological preserve that adjoins a 1/2 mile (1000 m) long cobble beach on Rosario Strait. The Marine Center also operates the Mosquito Pass Study Site, a 2.75-acre waterfront property located on the northwest corner of San Juan Island.

The recently-constructed Marine Education Center on the campus in Anacortes contains administrative and staff offices, a library and computer work area with spectacular views of Rosario Strait, and state-of-the-art Marine Chemistry and Instrumentation Laboratories.

The adjoining Sundquist Laboratory contains instructional laboratory space, a student project laboratory, culture facilities, research laboratories, microscopy facilities, and office space for staff and visiting researchers. A flow-through seawater system in the Sundquist Laboratory as well as outdoor tidal tanks provide areas for maintaining marine organisms.

The Shannon Point Marine Center also has a lecture hall and instructional computer laboratory, a dive locker, and a shop. The Marine Center's boats include a newly-constructed 26' research vessel, the 26' RV Fauna, the 20' RV Flora, as well as several smaller boats.

A 12-room, 24-bed dormitory provides accommodations for students and visiting scientists. The residential facilities also contain a Commons area with a kitchen where residents can prepare their meals.