[3] The stream's headwaters begin on the northern slopes of Mount Tamalpais in the Coast Range and terminate in southeast Tomales Bay, 1.5 miles (2.4 km) northwest of Point Reyes Station, California.

[5] To the Coast Miwok the stream was known as Tokelalume, then by the Spanish as Arroyo de San Geronimo, then Daniels creek.

[7] The creek's source is the northern slope of Mount Tamalpais, a few miles (~6–8 km) east of Bolinas Lagoon.

Shortly after this confluence, Lagunitas turns westward and flows through the town of Point Reyes Station.

[5] Most of its major tributaries are dammed, including the Kent, Alpine, Bon Tempe, Lagunitas, and Nicasio reservoirs.

Sedimentation from Lagunitas Creek into Tomales Bay resulted from nineteenth century logging and cattle grazing of riparian plants which otherwise slow erosion.

The Lagunitas Creek Watershed [1] is home to the largest remaining wild run of coho salmon (Oncorhynchus kisutch) in Central California.

These coho are part of the "Central California Coast Evolutionarily Significant Unit," or CCC ESU, and are listed as "endangered" at both the state and federal level.

[11] Strong efforts are also being made to protect and restore undammed, headwater reaches of this Watershed in the San Geronimo Valley, where upwards of 40% of the Lagunitas Creek salmon spawn each year and where as much as 1/3 of the juvenile salmon (or fry) spend their entire freshwater lives.

The Salmon Protection and Watershed Network ([1]) leads winter tours for the public to learn about and view these spawning salmon, and also leads year-round opportunities for the public to get involved in stream restoration, monitoring spawning and smolt outmigration, juvenile fish rescue and relocation in the summer, and advocacy and policy development.