established the California Cooperative Sardine Research Program, with the goal of studying the distribution and natural history of sardines, their availability to the commercial fishery, fishing methods, and the physical, chemical, and biological oceanographic processes influencing sardine populations in the coastal waters of California. Members of the program included the California Department of Fish and Game, the Federal Bureau of Commercial Fisheries, Hopkins Marine Station, the California Academy of Sciences, and Scripps Institution of Oceanography. The program was renamed the California Cooperative Oceanic Fisheries Investigation in 1953, when its scope was expanded to include other species besides the sardine.

Over time, the program's objectives evolved until, by 1960, they were primarily to understand the factors controlling the abundance, distribution, and variations of pelagic marine fishes. A major emphasis was on comprehending the physical and biological oceanographic processes affecting marine life in the California ocean current system as a whole (Baxter, 1982).

Even though the 1976 Fisheries Conservation and Management Act (FCMA) gave the federal government management authority over commercial fisheries in the exclusive economic zone (3 to 200 nautical miles from shore), the National Marine Fisheries Service (NMFS), the California Department of Fish and Game, and Scripps decided in 1979 to continue the CalCOFI program as a long-term marine resources monitoring and research program (Radovich, 1982).

The CalCOFI program measures a variety of biological and physical oceanographic variables. Plankton and neuston tows are used to collect ichthyoplankton, invertebrate zooplankton, and phytoplankton. Rapid postcruise measurements of zooplankton biomass are made, and some investigators work up the samples to greater levels of taxonomic detail. Primary production is measured daily; continuous measurements of temperature, light, chlorophyll, and dissolved oxygen are taken; and Acoustic Doppler Current Profiles of current measurements and acoustic back-scatter are collected. Chlorophyll, phaeophytin, salinity, dissolved oxygen concentration, nitrate, nitrite, phosphate, silicate, and water transparency data (to depths exceeding 500 m) are taken from a 20-place salinity-temperature-depth (also known as CTD) rosette on a grid of about 70 stations quarterly during the year. These measurements have been taken regularly for the past 44 years, using the technologies current at the time. Each spring, special egg and larval surveys are undertaken to determine the spawning biomass of certain commercially significant species of fishes.