The North Coast Railroad Authority (NCRA) was formed in 1989 by the California Legislature under the North Coast Railroad Authority Act, which was intended to ensure continuation of railroad service in Northwestern California. In 1992, the State purchased the railroad line from Willits north.  In 1995, the State then added the railroad line from Healdsburg north to the NCRA's holdings and provided for a joint powers authority, the Northwestern Pacific Railroad Authority (NWPRA) to own the right of way from Healdsburg south to Schellville in Sonoma County, where the railroad then feeds a 12-mile shortline through Napa County which connects to the Union Pacific mainline at Fairfield-Suisun in Solano County.

The NCRA has an easement that gives it the right to operate freight trains on the Sonoma-Marin Area Rapid Transit (SMART) tracks north of Highway 37 in Novato. Freight service has begun and trains are now running through Novato several times per week.

In Marin, the right-of-way runs through substantial areas of sensitive wetlands, marshlands and wildlife habitat.