The first European land exploration of Alta California, the Spanish Portolà expedition, camped near the river for two nights, in the vicinity of today's community of Watsonville, on October 8–9, 1769.

Franciscan missionary Juan Crespí, traveling with the expedition, noted in his diary that they "found half the body of a very large black bird, hanging [from] poles" (possibly a condor).

[3] In 1953 the State Water Resource Control Board determined that the Pajaro Valley Watershed suffered from saltwater intrusion due to groundwater overdraft.

By the 21st century, 54 square miles of the Pajaro Watershed's groundwater supply was overdrawn and as a result, below sea level making the area susceptible to saltwater intrusion.

In 1963, the USACE (United States Army Corps of Engineers) acknowledged poor planning in levee design, and congress authorized re-construction of the flood control system, however no funds were provided from the federal government.

[11][12] The Salinian Block rests above the Pacific Plate which slips north along the San Andreas Fault.

[14] The 1989 Loma Prieta earthquake in the Santa Cruz Mountains deformed the Pajaro levee system.

[14] A. R. Wilson Granite Rock quarry is located by the Pajaro gap adjacent to the river in San Benito County.

The Pajaro River mainstream flows west for 30 miles (50 km), passing the city of Watsonville and emptying into Monterey Bay.

The San Andreas Fault divides the watershed and is responsible for altering historical flow paths.

[19] A residential development, agricultural fields, and Zmudowski State Beach border the Pajaro River mouth and the connecting Watsonville Slough.

Western pond turtles (Actinemys marmorata), pallid bat (Antrozous pallidus), burrowing owls (Athene cunicularia), dusky-footed woodrat (Neotoma fuscipes), least Bell's vireo (Vireo bellii pusillus), and the yellow-breasted chat (Icteria virens).

Steelhead trout, the California red-legged frog (Rana draytonii), the Northern tidewater goby (Eucyclogobius newberryi,), and the snowy plover (Charadrius nivosus), which nests at the Pajaro river mouth at Zumdowski State Beach at the Pacific Ocean.

[25] Native California fish present in the lower Pajaro River are: three-spined stickleback (Gasterosteus aculeatus microcephalus), Sacramento perch (Archoplites interruptus), riffle sculpin (Cottus gulosus), Russian River tule perch (Hysterocarpus traskii traskii), South Central California Coast steelhead trout (Oncorhynchus mykiss), and thicktail chub (Siphatales crassicauda).

[27] In 1953, local Gilroy resident, Herman Garcia Sr., caught a Chinook salmon in the Uvas Creek tributary of the Pajaro River.

However, citizen naturalist and author William "Bill" Leikam reported salmon in Corralitos Creek while fishing for steelhead trout in 1956 in the reach along Freedom, California at the season's first large winter storms.

[17] Also noteworthy is perhaps the southernmost record of North American river otter (Lontra canadensis) in a California coastal watershed.

In 1969 river otter were recorded eating freshwater mussels (California floater (Anodonta californiensis)) on the Santa Ana Creek tributary of Tequisquita Slough, 2 miles east of Hollister.

The project begins at Murphy's crossing, and extends 7.5 miles westward to the Pacific Ocean ending before highway 1.

It is also intended to preserve and restore habitat corridors linking the Santa Cruz, Gabilan, and Mt.