Founded in 1903 and incorporated into the University of California system in 1912, the institution has since broadened its research focus to encompass the physics, chemistry, geology, biology, and climate of the Earth.

With funds secured from Ellen Browning Scripps, the association was able to have a ship built by Lawrence Jensen strictly for oceanographic research - among the first for an American nongovernmental institution.

In 1935, SIO director T. Wayland Vaughan was the first Scripps member to be awarded the Alexander Agassiz Medal by the National Academy of Sciences.

[21] With Harald Sverdrup as the SIO director, recent graduate student Walter Munk was recalled from the army and together they were tasked with aiding Allied amphibious landings off the coast of Africa.

[26] Though Sverdrup was initially intending on holding the position of SIO director for only 3 years until 1939, Nazi occupation of Norway prolonged his assumption of the role until 1948.

UCDWR research led to rapid development of bathythermographs, as well as the understanding of the thermocline and benthic sediments in the context of underwater warfare.

[28] Research on biofouling organisms were led by Dennis Fox and Claude ZoBell, with the goal to develop biological deterrents for seaplanes and vessels.

SIO's first scientific diver was biologist Cheng Kwai Tseng, who used equipment to collect algae off the coast of San Diego in 1944.

[29][30] Tseng took red algae samples of Gelidium cartilagineum and cultured them to reduce the US dependence on Japanese agar, which was important to hospitals at the time.

[33] The three new vessels were put to work on the new Marine Life Research Program in 1950 (now CalCOFI), which sought to investigate the collapse of the California sardine population.

When Aqua-Lung was made available in the US in 1948, UCLA graduates Conrad Limbaugh and Andy Rechnitzer were able to convince Boyd W. Walker, their marine biology advisor at the time, to purchase one.

[35] The Vaughan Aquarium-Museum opened at the University's Charter Day in March 1951 to replace the prior aquarium, which had been in a consistent state of disrepair since at least 1925.

[11] Named to honor former institution director T. Wayland Vaughan, museum curator Percy S. Barnhart planned a replacement up until his retirement in 1946, passing the project along to Sam Hinton.

While nearly three times the size of the previous aquarium, the building also housed the director's offices on the second floor and the preserved specimens in the basement.

In 1965, Scripps began leasing 6 acres (2.4 ha) of land in Point Loma to tie up research vessels, including the RP Flip (launched in 1962), from the US Navy.

[46] Scripps, along with NOAA as the sole American members of the science committee, has overseen and advised many expeditions to contribute to the global data set.

[50] From January to May of 2019, SIO directed a study at Imperial Beach to collect samples of sewage pollution from the Tijuana River and found elevated levels of harmful bacteria and aerosols.

[51][52] In 2024, Scripps was added to a task force including researchers from San Diego State University and regional doctors to better understand health impacts from the pollution.

In June 2023, two SIO students and one recent graduate were arrested at their homes by University of California Police and held in custody overnight.

On July 18, 2023, UCPD obtained a warrant and searched a fourth student's house for evidence of chalk or union affiliation in relation to the May 30 incident.

[69] Biological Grade is the street running North to South parallel to La Jolla Shores drive, connecting a number of laboratories, libraries, and research halls.

[72] Shellback Way connects a series of halls and labs on the east side of La Jolla Shores Drive, with greater emphasis on atmospheric science and fisheries.

[72] (Nori, Rockweed, Limu, Kelp, Eelgrass, Corallina) The main campus in La Jolla is situated next to the San Diego-Scripps Coastal Marine Conservation Area as well as Torrey Pines State Natural Reserve.

[86] The Nimitz Marine facility is the home port of all SIO research vessels and is accessible by land via Rosecrans Street in Point Loma.

The facility is serviced hourly by bus route 84 of the San Diego MTS, running from the Navy Base to Shelter Island and Cabrillo National Monument.

[96][97] Spearheaded by Charles David Keeling, SIO established a research center in Mauna Loa, Hawaii to record atmospheric carbon dioxide levels.

[101][102][103] SIO also has a geological collection of thousands of ocean cores, sea dredge hauls, microfossil slides, and rock samples.

Scripps chose Seattle-based architect Glosten as the ship's designer, having work experience from numerous other SIO vessels.

Birch Aquarium, the public exploration center for the institution, features a Hall of Fishes with more than 60 tanks of Pacific fishes and invertebrates from the cold waters of the Pacific Northwest to the tropical waters of Mexico and the IndoPacific, a 13,000-gallon local shark and ray exhibit, interactive tide pools, and interactive science exhibits.

(Latin: "friends with praise") In 2014, the institution and its Keeling Curve measurement of atmospheric carbon dioxide levels were featured as a plot point in an episode of HBO's The Newsroom.