The Marine Physical Laboratory's (MPL) business office, research and development machine shop, some of its laboratories, and UC San Diego's classified research security office are located on a secured Space and Naval Warfare Systems Center (SPAWAR) facility within Naval Base Point Loma, 13 miles south of the main UC San Diego campus. These facilities are adjacent to the Nimitz Marine Facility, home port to R/P FLIP, and the rest of the Scripps oceanographic research fleet.

In addition to Point Loma, MPL also utilizes their La Jolla facilities located on the Scripps Institution of Oceanography campus over looking the Pacific Ocean.