The creek mouth area contains slough and wetland habitats including mudflats that are known habitat of the endangered California clapper rail. San Mateo Creek was federally designated in 2002 as a section 303 impaired watershed for the substance diazinon; however, diazinon has been banned for golf course use by the U.S. Government. There is one golf course that provides surface runoff to San Mateo Creek in the city of San Mateo, and Crystal Springs Golf Course that drains to the Crystal Springs Reservoir.