The railroad used ferries of San Francisco Bay for freight transfer until connected to the national rail network at Napa Junction by the Santa Rosa and Carquinez Railroad in 1888. The Santa Rosa and Carquinez remained part of SP independent of the NWP with a primary freight interchange at Schellville. SP's Santa Rosa branch continued from Schellville through Sonoma to a separate terminal yard on North Street in Santa Rosa. Freight interchange was predominantly through Ignacio, but there was a second connection to the SP in Santa Rosa until the line through the Valley of the Moon was abandoned in 1935.