The San Pablo Creek watershed is one of the largest and most geographically diverse in the East Bay, draining 41 square miles and ranging from near-pristine oak woodlands in portions of the upper watershed to the suburbanized and urbanized lands above and below San Pablo Dam.
At San Pablo Dam, the creek drains 23.37 square miles, or slightly over half of the entire watershed. Below the dam, from both north and south of San Pablo Dam Road, more tributaries flow into the creek as it meanders through semi-rural El Sobrante, providing a soothing contrast to the rapid pace of San Pablo Dam Road traffic. It then flows openly through San Pablo, paralleling Wildcat Creek for much of its length, and finally through North Richmond before entering the Bay.

As it reaches the Bay, San Pablo Creek flows into 300-acre San Pablo Creek Marsh, home to endangered species such as the California clapper rail and the salt marsh harvest mouse, the threatened and highly secretive black rail, and the salt marsh wandering shrew and San Pablo vole, both species of concern. Another secretive bird, the salt marsh song sparrow, sings from the edges of the marsh's sloughs, while salt marsh yellow-throats flit among the willows and rushes where the creek transitions from fresh to salt water.