The first European land exploration of Alta California, the Spanish Portolà expedition, traveled along the coast on its way north, and again on the return.

[5] In 1995 a review of coho south of San Francisco Bay found coho restricted to only one remnant population in Waddell Creek, one small naturalized (hatchery-influenced) population in Scott Creek and a small hatchery-maintained, non-native run in the San Lorenzo River, all in Santa Cruz County.

Historically, coho were found in approximately 50 coastal drainages in San Mateo and Santa Cruz counties, but by the 1960s spawning runs were limited to 11 stream systems.

Juvenile starry flounder (Platichthys stellatus) and Pacific staghorn sculpin (Leptocottus armatus) are infrequently observed in the estuary.

[9] The lower Scott Creek watershed flows through the 3,200 acres (1,300 hectares) Swanton Pacific Ranch, managed by California Polytechnic State University.