Fishes of southern California coastal streams and associated coastal lagoons live with a Mediterranean-style hydrological cycle. Winter rains open the lagoons to the ocean; subsequent dry season low flows and changes in sandy beach dynamics closes them for most of the year. Artificial breaching of barrier sand berms can disrupt fish populations and cause mortality. Such breaches have been rarely observed and then only after some time has passed. An artificial breaching at the mouth of the Santa Clara River, Ventura County, CA coincided with an extreme low tide on 17 September 2010. We observed the mortality of thousands of both native and non-native fishes and invasive frogs; including at least thousands of the federally endangered Tidewater Goby (Eucyclogobius newberryi) and seven smolts of the federally endangered southern Steelhead (Oncorhynchus mykiss). Despite the many anthropogenic, faunal, and non-faunally related reasons for breaching, our observations confirm such actions can be detrimental to conservation and recovery of threatened and endangered species as well as to other fauna and flora dependent on such habitats.