At 26.6 miles (42.8 km),[2] it is the longest stream in San Mateo County and flows all year from springs in the Santa Cruz Mountains.

In early Mexican land grants or disueños, John Gilroy stated "The Castros, I and an Indian gave it that name in 1814, being a place where we used to catch salmon.

When the Portolà Expedition traveled on horseback along the immediate coast on October 24, 1769, Padre Juan Crespí wrote, "Only in the watercourses are any trees to be seen; elsewhere we saw nothing but grass, and that was burned."

The sawmill employed fifty to eighty men manufacturing sixty-thousand board foot of redwood and Douglas fir lumber daily.

A forest railway was extended more than 7 miles (11 km) up Pescadero Creek to bring logs down to the sawmill after loggers had felled all trees close enough to be winched to the mill with cables.

In the early 1960s local farmers used a dragline to remove sediment from Butano Creek channel below Pescadero Bridge for several thousand feet down stream.

Intensive logging and watershed development, also beginning in the late 1920s or early 1930s, has dramatically increased sedimentation in Butano and Pescadero creeks.

[5] Before logging removed much of the dense forest cover of this area in the middle of the 20th century, these streams were shaded, with frequent, stable pools created by fallen trees, bedrock outcrops, and boulders, and an abundant, if not steady, supply of gravel.

[5] According to a study by Professor Jerry Smith of San Jose State University, estimates in 1985 showed that 10,000 steelhead trout were rearing in the lagoon.

[11][12] Contrary to popular myth, most beaver dams do not pose barriers to trout and salmon migration, although they may be restricted seasonally during periods of low stream flows.

[14] Beaver sign (Castor canadensis) was recently documented in the newly restored Butano Creek channel just above the Pescadero lagoon in September, 2022 (See photo).

Besides being a refuge and nesting ground for wintering waterfowl, the marsh is a critical spawning area and nursery for coho salmon, steelhead trout, tidewater goby, and many other threatened or endangered fish, amphibian, and reptile species.