RTC's main research facility is located in the historic Navy Net Depot warehouse. Laboratories, offices, classrooms and other elements of the physical plant, and an open bay of 12,000 sq ft are housed within this structure. An award by the NSF ARI Facilities Modernization Program of $1.6 million and an accompanying $700,000 SFSU match enabled the modernization of this building, providing funds to renovate existing laboratories and capture five new laboratory spaces and to upgrade all safety aspects of the building. Phase II of the renovation of this building, a $3.2 million project, added new laboratories, offices, classrooms and needed infrastructure. It was funded by a combination of private foundation awards (W.M. Keck and Marin Community Foundation) and a federal appropriation to the National Estuarine Research Reserve (NERR) program and the RTC.

The Ecology and Aquarium Facility (12,000 sq ft) has significant space for seawater tables and tanks. This building also has laboratory and office space for RTC faculty and students and houses the San Francisco Bay Environmental Assessment Monitoring (SF-BEAMS) Project, and the California 's Coastal Ocean Current Monitoring (COCMP) Program. The Center has constructed an marine organism culture room (700 sq. ft., located in the main research facility), which is temperature and light-controlled and has running Bay water.

Located on the RTC seawall is a newly renovated combination greenhouse and research wet lab (1500 sq. ft.) with running bay water for maintaining plants and invertebrates. The RTC Bay water system has been upgraded through support from an NSF FSML award. A 300 foot tethered intake line has been constructed offshore in San Francisco Bay, and a computer controlled mixing and delivery system is in the design phase.