This lists includes birds found along the river from Highway 1 downstream to the river mouth, as well as birds found in adjacent areas including San Lorenzo Park, the eucalyptus trees growing on the bluff by the train trestle near the river mouth, and the small creek running from the end of South Branciforte Ave.

The lower three miles of the river was channelized by the U.S. Army Corps of Engineers between 1957-59. Today paved paths run along the levees on each side of the river except for a section on the east bank between the Soquel Avenue Bridge and the area by the Santa Cruz County Courthouse. The river is tidal up to about the Water Street Bridge except when sand bars close off the river mouth.