Patterns of abundance were documented for 17 species of fish in the lagoon at the mouth of San Mateo Creek, northern San Diego County, California from occasional observations (1974-1997) and multiple samples per year (1998-2008). Fish populations varied with Mediterranean climate patterns of rainfall, stream flow and consequent breaching of the lagoon to the ocean through the barrier sand berm. Two near-record rainfall seasons occurred during this period; the 1997-1998 El Niño due to southern storms and the 2004-2005 winter wet season of more usual storms from the north and northwest. The lagoon stabilized as fresh to brackish in the dry season and for multiple years during successive drier winters. Closed conditions benefitted the native, federally endangered southern tidewater goby, Eucyclogobius kristinae, but were less suitable for other native estuarine species more common in wetter years. Wet year flows also reduced non-native freshwater species; some thrived and increased predation pressure on the southern tidewater goby. Historically these exotics were absent and two additional native species were present, partially armored threespine stickleback, Gasterosteus aculeatus, and the federally endangered southern steelhead, Oncorhynchus mykiss. Restoring and maintaining a full suite of native species will require a combination of 1) habitat maintenance and restoration, 2) control or management of non-native species, and 3) reintroduction of some native fishes and amphibians.