San Gregorio Creek begins where Alpine Creek and La Honda Creek converge in the hamlet of La Honda, then flows 11.8 miles southwest through rolling grasslands and pasturelands to its mouth at San Gregorio State Beach. Along the way, it passes through the unincorporated communities of La Honda, San Gregorio, Redwood Terrace, and Sky Londa, gathering water from more than a dozen tributaries with names that echo the region's layered history: Harrington Creek, El Corte de Madera Creek, Bogess Creek, Spanish Ranch Creek. The creek was called Arroyo de San Gregorio in Spanish times and Arroyo Rodrigues in the 1850s. It is designated California Historical Landmark number 26, marking the spot where the Portola expedition camped in October 1769.

At its mouth, San Gregorio Creek forms a seasonal lagoon behind a sand berm just upstream of the Highway 1 bridge. At its largest, this lagoon covers about five acres and reaches six feet deep, a small but critical body of water that serves as nursery habitat for tidewater goby and rearing steelhead. Coho salmon smolts use the lagoon differently, pausing there to physiologically prepare their bodies for the transition from fresh to salt water before migrating to the open ocean. During winter rains, the creek often cuts through the sand berm and flows directly into the Pacific. In drier months, water seeps invisibly through the sand. This rhythmic cycle of barrier and breach shapes the lagoon's ecology and determines which species can use it in any given season.

A 2008 survey found both coho salmon and steelhead in San Gregorio Creek but identified Highway 84 bridge culverts as one of the most immediate threats to their survival. At three sites, culverts impede fish passage during low flows. At a fourth, a small tributary culvert is completely impassable in any season, cutting off habitat upstream permanently. Sedimentation from residential development, grazing, and logging compounds the problem. In 1993, water rights in the watershed were adjudicated and a minimum bypass flow was established, but scientists noted the prescribed flows were too low to sustain viable coho populations. The California Department of Fish and Game targeted the watershed for salmon recovery in 2007, and a 2010 management plan focused on four special-status species: California red-legged frog, coho salmon, steelhead, and tidewater goby.

The creek's watershed shelters more than troubled fish. Western leatherwood, Santa Cruz manzanita, and King's Mountain manzanita -- all listed in the California Native Plant Society's Inventory of Rare and Endangered Plants -- grow in the La Honda Creek Open Space Preserve that flanks the upper watershed. These plants are specialists, adapted to the particular combination of fog, soil, and slope that the Santa Cruz Mountains provide. The watershed remains primarily pastoral, with cattle grazing, timber harvesting, and recreational trails as its main commercial uses, but residential development has been increasing steadily. The tension between the watershed's ecological value and its real estate potential defines the creek's future as surely as its hydrology does.