Observations beginning in 1974 and later surveys of increasing intensity with small seines, traps, and dipnets (1991 to mid-2008) documented patterns of abundance, colonization, and extirpation of 15 species of native and non-native fishes as well as crayfishes, and amphibians in the lagoon at the mouth of San Mateo Creek, northern San Diego County, California. Fish populations varied with Mediterranean climate patterns of stream flow and 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 dry winters. Closed conditions benefitted the native, federally endangered Southern Tidewater Goby, Eucyclogobius n. sp., but were unsuitable for other native estuarine species more common in wetter years. Wet year flows also brought down non-native freshwater species to the lagoon; some thrived and increased predation pressure on the tidewater goby. Historically these exotics were absent and two additional native species were present in the lagoon, Partially Armored Threespine Stickleback, Gasterosteus aculeatus, and the now federally endangered Southern Steelhead, Oncorhynchus mykiss. Restoring and maintaining a full suite of native species will require a combination of 1) habitat maintenance, 2) control or management of non-native species, and 3) reintroduction of some native fishes and amphibians to restore the faunal communities of remaining small coastal estuarine systems.