The Santa Margarita River watershed stands alone in southern California as having an unbroken, unchannelized corridor of lowland riparian habitat along its floodplain from its headwaters to an intact coastal estuary at its mouth. With most of its 27-mile length skirting the southern border of vast Camp Pendleton (DoD), it has survived the major modification of its banks for agriculture and urbanization that has affected virtually every other lowland river in Central and Southern California. North of the river, within Camp Pendleton, the rugged hills of the southern Santa Ana Mountains provide important habitat for the remaining wide-ranging megafauna of coastal southern California, including Mountain Lion. The base is also home to over 95% of the endemic Pacific Pocket Mouse (Perognathus longimembris pacificus), restricted to sandy soils on marine terraces. Other important habitat features for birds within this IBA include the tributaries Sandy Creek and De Luz Creek, as well as San Mateo Creek on the northern border of Camp Pendleton and O'Neil Lake, one of the most extensive freshwater marshes along the coast of southern California. The headwaters of the Santa Margarita are the site of intensive ecological research (through California State University, San Diego) and conservation efforts to connect with the Peninsular Ranges of western Riverside and northern San Diego County via the Tenaja Corridor.
The most outstanding feature of the avifauna of the Santa Margarita River watershed is the veritable abundance of many species that are otherwise reduced to scattered pairs in the region. Predictably, the diversity of breeding species is remarkable around 90 taxa within a 10-square-mile block (KW). For riparian bird species, the population of Least Bell's Vireo is by far the largest in the state, with over 300 pairs in 1993, and that of Southwestern Willow Flycatcher (18-25 pr.) is one of the three largest in the state away from the Lower Colorado River, the others being on the San Luis Rey River and the South Fork Kern River (Stephenson and Calcarone 1999). Its population of Long-eared Owl, once abundant in willow thickets bordered by grassland throughout southern California, is now apparently the only one left along the coast (west of I-5). The extensive grassland supports multiple territories of Northern Harrier (by comparison, <10 pairs breed in all of Los Angeles and Orange County each year). Several distinct core populations of California Gnatcatcher (USFWS, unpubl. data) occur along the River. The estuary at the mouth of the Santa Margarita River is equally impressive, with possibly the largest breeding colony of California Least Tern in the world (1064 nests in 2001); one of state's largest populations of breeding Snowy Plover (89 nests in 2001); as well as over 100 pairs of Belding's Savannah Sparrow. More than 1500 shorebirds per day refuel at the river mouth during the fall (Page and Shuford 2000). The lack of public access has been important for the low level of disturbance to these species, but more critical has been the fact that development has been so limited within the borders of the base, in sharp contrast to everywhere else along the coastal plain of southern California (all bird survey numbers B. Foster, unpubl. data).
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The explosion of population growth in western Riverside Co. (headwaters of the Santa Margarita River) have resulted in unprecedented invasions of exotic plants throughout the river system (esp. Arundo and Tamarisk). Feral cats are a local but growing problem along the river, and education programs would be warranted around developed areas within the upper watershed (e.g. Fallbrook). Channelization proposals for tributaries of the Santa Margarita (e.g. Murrieta Creek) remain a constant threat to riparian habitat, and powerline construction proposals threaten to encourage exotic species invasions into intact habitat. Though the habitat on Camp Pendleton is secure for now, it receives no formal protection as an ecological reserve or wildlife refuge, and should be considered at risk from future development schemes. Recently, residential development on the base has claimed several hundred acres of coastal sage scrub and grassland habitat.
The Santa Margarita River watershed stands alone in southern California as having an unbroken, unchannelized corridor of lowland riparian habitat along its floodplain from its headwaters to an intact coastal estuary at its mouth. The estuary and salt flats at the mouth of the Santa Margarita River is equally impressive.