Plants Supporting a highly productive ecosystem, the San Mateo Creek watershed includes a high variety of elevations and vegetation groups. These include
riparian zones and
woodlands around the perennial or semi-perennial streams,
grassland on the valley floors, and
chaparral and
coastal sage scrub on the hillsides. Overall the vegetation groups and their distribution are very similar to that of San Juan Creek and its major tributary,
Trabuco Creek, in the northwest. The major difference is that the San Mateo Creek watershed contains no major residential areas. The mouth of the creek and its last reaches shortly above and below Camp Pendleton are host to a wide variety of riparian plants. At the mouth, there is a freshwater lagoon and several freshwater marshes, surrounded by a riparian woodland consisting primarily of
willow,
sycamore,
live oak and
cottonwood. Surrounding the lower San Mateo Creek valley and on the shallow slopes is the coastal sage scrub community, which consist primarily of
coast goldenbush,
coyote brush,
California sagebrush,
mulefat,
toyon,
poison oak,
laurel sumac,
California mugwort,
Mexican elderberry, and
California encelia. At the very mouth, where
groundwater surfaces on the streambed, there are the stands of trees, and undergrowth includes
wild cucumber and
gooseberry.{{cite web Freshwater marshes surrounding San Mateo Creek exist in a strip just a few hundred feet wide and draw their water supply primarily from emerging groundwater. The most prominent plants are
bulrush, specifically
California bulrush, and
cattail. There are also several species of
burweeds and
ferns, and on the edges of the marshes and on the surrounding small meadows,
goldenrod,
hedge-nettle,
fleshy jaumea,
Mexican rush,
saltgrass, and
iceplant.
Animals In February, 1999,
steelhead (
Oncorhyncus mykiss irideus) were discovered in the creek by Toby Shackelford, making San Mateo Creek the only watercourse south of
Malibu Creek in
Los Angeles County with steelhead in the endangered
Southern California Steelhead DPS.{{cite news Steelhead have historically spawned in the creek, whose upper reaches also support a population of
coastal rainbow trout, the stream resident form of
O. m. irideus. There are about of streams in the watershed that provide suitable habitat for steelhead.{{cite web Significantly, DNA analysis has shown that San Mateo Creek steelhead are genetically native southern steelhead, and not hatchery stocked fish. Steelhead in San Mateo Creek spawn primarily in the winter, when heavy storm runoff from the Santa Ana and Santa Margarita Mountains raises the creek's flow enough to breach the sandbar at
San Onofre State Park. In the few weeks or months following when there is still a substantial flow in the creek, the steelhead spawn and then the adults return to sea. In the dry months following the streams in the lowlands shrink to small pools that still support
amphibians and small fish including steelhead fry which need to spend about one year in freshwater. Recently, steelhead have been sighted in the creek in greater numbers, bringing attention to coastal San Diego and Orange County streams.{{cite web Other fish and amphibian species in the watershed include the endangered
tidewater goby and
arroyo toad. Tidewater goby reside in small to medium-sized, brackish sloughs and marshes near the mouth of the creek. The watershed also has a number of birds; endangered species include the
least Bell's vireo (
Vireo bellii pusillus),
California gnatcatcher (
Polioptila californica) and
willow flycatcher (
Empidonax traillii). In early February, 2010 a
golden beaver (
Castor canadensis subauratus) was captured in a live trap by
San Onofre State Beach officers who discovered the beaver at the river mouth of San Mateo Creek. According to State Parks officials, the species was once native to the San Mateo Creek watershed, but were thought to be extinct.{{cite news Beaver were also found in an ecological survey of the lagoon near the creek mouth in 1987.{{cite report |title=Trestles Wetlands Natural Preserve Habitat Restoration Plan A report on the fauna of the county by Dr. David Hoffman in 1866 stated "Of the animal kingdom we have a fair variety: the grizzly bear, the antelope, the deer, the polecat, the beaver, the wildcat, the otter, the fox, the badger, the hare, the squirrel, and coyotes innumerable."{{cite journal The beaver may have accessed San Mateo Creek from the
Santa Margarita River watershed where golden beaver were re-introduced around 1940.{{cite journal ==History==