Santa Margarita River Estuary

GENERAL			Source
Site	Santa Margarita River Estuary
Map	Oceanside USGS 7.5' quadrangle
Location	The estuary is located at the mouth of the Santa Margarita River in northern San Diego County approximately 1 mile north of the City of Oceanside. It is at the southwestern corner of the Camp Pendleton Marine Corps Base.
Contacts	U.S. Marine Corps Base Camp Pendleton, (619) 725-4512/4524
	U.S. Environmental Protection Agency, (415) 744-1985
	U.S. Fish and WIldlife Service, Carlsbad Field Office, (619) 431-9440
Approximate Wetland Acreage	192		4
Approximate Historic Acreage	839		13

Ownership	Owner	Acres	Source
	U.S. Marine Corps Base, Camp Pendleton	265	2

LAND USE			Source
Land Use Designation	The estuary is within the area designated military base in the County's General Plan and Zoning Ordinance. Within Camp Pendleton it is a Special Management Zone.		7, 17
Onsite Use	Interstate 5 and the railroad cross the estuary. All land within the Base is used for military training compatible with maintaining ecological integrity. Scientific research, limited hunting and other recreation are allowed with a permit from the Base.		2, 12, 17
Historic Use	The floodplain was cultivated prior to 1942. Secondarily treated sewage effluent was released into the estuary from the 1940's through the early 1970's. Until 1970, salt flats were used for tank training exercises.		3, 2, 16, 17
Adjacent Use	Camp Pendleton Marine Corps Base uses the areas to the north, east, and northwest of the estuary for military training. Areas to the north of the estuary are leased for agriculture.		12
Historic Adjacent Use	The Marine Corps Base was established in 1942; prior to that surrounding lands were used for crop production and cattle ranching.		2, 16, 17

HYDROLOGY			Source
Tidal Influence	The ocean inlet is not constricted by man-made structures, but inland from the mouth, tidal influence is constrained by rock jetties from I-5 and the railroad crossings. The inlet may be open or closed for extended periods depending on rainfall and flows.		2, 3, 17
Watershed Area	740 square miles		1

Tributaries and Flow	Tributary	Flow	Source
	Santa Margarita River	Flows vary seasonally; the highest recorded flow 1923-1990 was 33,600 cfs near Ysidora. It is the longest free flowing river in coastal southern California; the channel is braided and supports the most extensive riparian corridor in the county.	1, 16, 20
Dams	Lake O'Neill is out of the River channel but receives much of its water from seasonal River diversions; two additional dams are located in the upper watershed along the two streams which join to form the Santa Margarita River.		1, 3, 17
Other Sources	Runoff and groundwater seepage also contribute water to the estuary.		1, 16

WATER QUALITY			Source
General	Included in San Diego Regional Water Quality Control Board 1996 draft list of impaired water bodies; selected standards exceeded for eutrophication. Beneficial uses are rec1, rec2, est, wild, rare, mar and migr.		5, 6
Dissolved Oxygen (DO)	1986, 87- Data were collected at 7 stations in the estuary, 5 times over the year; the mouth was closed after the 2nd sampling. DO levels ranged from 2.5 to 17.0 mg/l over the period. The temperature range was 16 - 29.5 C.		4
	Time and depth of collection were not indicated.
Water Salinity	1986, 87- Data were collected at 7 stations in the estuary, 5 times over the year; the mouth was closed after the 2nd sampling. Salinities ranged 1.5 to 30 ppt (depth of sample not indicated). 1993 ranges were comparable.		4, 15
Sediment	The average annual sand and gravel yield for the Santa Margarita river over a 25 year period (1950-1975) was estimated at 8,160 tonnes (a tonne is defined as a metric ton and equals 2,204.6 pounds).		3

Soil			Source
Soil	Soil at the estuary is predominantly a fine, gray-brown silty or sandy clay.		3

Habitat	Acres	Vegetation
Salt marsh	81	1988 - At lower elevations, dominated by common pickleweed and alkali heath. At higher elevations, salt grass and common pickleweed were dominant. The highest elevations in the salt marsh were dominated by glasswort.	4
Salt pan	98	1988 - pickleweed dominant, with scattered shoregrass, sea-lavender and alkali heath.	4
Brackish/fresh water marsh	5	1988 - highly variable, dominated by tule cattail; other species included western goldenrod, saltbush, marsh fleabane, mulefat, yerba mansa, fleshy jaumea and heliotrope.	4
Willow woodland	8	1988 - dominated by arroyo, sandbar, red, and black willow.	4
Upland	20+	1988 - Maritime scrub, coastal strand; 1996 beach and dune providing Ca Least tern nesting habitat.	4, 18, 19

ANIMAL USE			Source
Birds	1988 report - 207 species of birds known to have occurred at the estuary, 85 associated with open water, salt marsh or mudflats. 1992 report listed 18 sensitive wetland species found along the lower river and estuary,		1, 4, 9, 11, 18, 19
	including 3 breeding onsite: Ca. least terns#, 486 nests in 1995; Belding's Savannah sparrow#, 120 prs in 1991; western snowy plover#, 34 nests in 1994.
Fish	1993 - 22 species including 14 native estuarine and marine species caught in the lagoon; California killifish were abundant, also deepbody anchovy, topsmelt, bay pipefish, staghorn sculpin and striped mullet present; tidewater gobies+ were not found.		15, 4
	1986, 1987 - A total of 14 species of fish were caught using gill nets at five stations within the estuary. Topsmelt, California halibut, diamond turbot, and striped mullet were most abundant.
Benthic Invertebrates	1981 - 26 species of aquatic invertebrates were found at the estuary. Phyla present were ribbon worms, segmented worms, molluscs, and arthropods. Abundance estimates were not provided.		1, 3
Insect	1981 - limited data was available. Water boatmen found in saline and brackish pools.		3
Other Wildlife	1986, 87 - 6 species of reptiles, 2 amphibians, and 2 mammals were trapped at the estuary; 1981 - 15 species of mammals from 11 families were trapped or observed, directly or by track, including raccoon, coyote, gray fox and longtail weasel.		3, 4
Special Status Species	1992 report - California brown pelican, white-faced ibis, least bittern, osprey, golden eagle, bald eagle, sharp-shinned hawk, marsh hawk, prairie falcon, peregrine falcon, California least tern# (also 1995,) elegant tern,		1, 4, 8, 9, 11, 15, 18, 19
	western snowy plover# (also 1994), black skimmer, long-eared owl, willow flycatcher, Belding's Savannah sparrow#, and loggerhead shrike; alkali locoweed and California orcuttia.

OUTLOOK			Source
Enhancement Status	Enhancement projects implemented by the U.S. Marine Corps at Camp Pendleton include: dredging in 1971 to convert the brackish marsh along the north side of the estuary, to salt marsh and creation of a one-acre least tern nesting island in 1983.		2, 3
	As mitigation for a Navy project located at the Base, enhancement of the estuary is planned but no details were available as of January 1996.
Watershed Management	Various sensitive lands in the watershed have been preserved as open space and ecological reserve by both private and public landowners. Working with the US Fish and Wildlife Service, the Marine Corps has developed an ecosystem management		14, 12
	plan to ensure that Base training activities are compatible with endangered species habitat needs. Numerous studies and management projects include a cooperative effort among San Diego and Riverside counties, federal and state agencies and
	community groups to develop a watershed plan focusing on land uses, flood control, erosion, sedimentation and the long-term effects of urbanization on the river's habitats; other enhancement and education efforts are also underway in subwatersheds.
Pressure	Invasive exotic vegetation; development in the upper watershed and the potential for modifying river hydrology and increased sedimentation.		1, 17

Comments	Population data on sensitive species at Camp Pendleton is updated frequently.

SOURCES
1	Cadmus Group for the U.S. EPA. 1992. Technical support for wetlands advanced identification in California coastal watersheds, final report. 300 pp., plus appendices.
	This report was initiated by EPA to collect technical information and analyze the existing data on the Santa Margarita watershed and the wetlands within its boundaries. It includes an overview of data on the watershed, land use, groundwater,
	and sedimentation, an analysis of wetland functions, and recommendations on possible wetland assessment methodologies. No original field work was conducted for this study, however, new GIS map layers were produced.
2	California Coastal Conservancy. 1989. The coastal wetlands of San Diego county. 64 pp.
	Public education booklet describing ecological concepts and dynamics of San Diego County salt marshes. Discussion includes watershed processes, littoral and tidal influences, habitat types, significance to migratory
	birds, and the effects of urban development. Profiles the history, current values and problems, protection efforts and public access opportunities at 13 wetland areas.
3	U.S. Fish and Wildlife Service. 1981. Santa Margarita River Estuary resource values and management recommendations. 140 pp.
	This study was conducted to facilitate the development of fish and wildlife management recommendations for the Santa Margarita River Estuary. Field data was collected on topography, soil and water chemistry, tidal influence, and animal and plant
	distribution and abundance. It includes management recommendations.
4	U.S. Fish and Wildlife Service. 1988. Preliminary results of the resources inventory at the Santa Margarita River Estuary. 128 pp.
	This report summarizes the results of original field work at the Santa Margarita river estuary. Data on water quality, vegetation, aquatic invertebrates, amphibians and reptiles, birds and mammals is summarized. It also includes a discussion on
	the endangered bird species found at the estuary.
5	San Diego Regional Water Quality Control Board. 1994. Water quality control plan for the San Diego basin. Approximately 225 pp. and appendices.
	The plan designates beneficial uses and associated water quality objectives for inland surface waters, coastal waters, reservoirs and lakes and ground water in San Diego County. It includes a discussion of applicable policies and statutory requirements and identifies measures for achieving water quality objectives. It also describes ongoing monitoring and assessment programs. Appendices contain summaries of regional growth forecasts and criteria for organic and inorganic constituents requirements and identifies measures for achieving water quality objectives. It also describes ongoing monitoring and assessment programs. Appendices contain summaries of regional growth forecasts and criteria for organic and inorganic constituents..
6	San Diego Regional Water Quality Control Board. 1996. Draft 303(d) list.
	A proposed list of waterbodies in the San Diego Basin that do not or are not expected to attain water quality standards after application of required technology-based controls. Specifies selected beneficial uses and criteria assessed, and the percentage of samples in which criteria were exceeded. It also identifies waterbodies for which previous assessments are no longer applicable.
7	Fairbanks, Janet. San Diego Assocation of Governments (SANDAG). Personal Communication, December 8, 1995.
8	Holland, Dan C. 1992. The distribution of the Tidewater Goby on Camp Pendleton. Prepared for U.S. Marine Corps Base Camp Pendleton. 24 pp.
	Report on tidewater goby surveys conducted in 1990 and 1991 in 7 creeks and lagoons on Camp Pendleton. Results are compared to those of previous surveys and site-specific recommendations made for protecting and enhancing goby populations and their habitat. Describes habitat conditions in terms of water quality (no sampling), introduced predators, and surrounding land use.
9	National Biological Survey for the Department of Fish and Game and US Fish and Wildlife Service. The status of western snowy plovers in San Diego County. 1994. 16 pp.
	The overall objective of this study was to determine the use of southern California's coastal wetlands habitats by western snowy plovers during the breeding and wintering seasons. The ability of the wetlands to support viable populations of western snowy plovers will be evaluated at the end of the research. This report includes the results of the first year of a three year survey.
10	US Fish and WIldlife Service for the US Navy, Natural Resources Management Branch. 1987. A survey of Belding's savannah sparrows in California, 1986. 20 pp.
	This report summarizes data collected on Belding's savannah sparrows at 30 marshes along the California coast. The purpose of the study was to provide an update on the status of the Belding's savannah sparrow in California, document the current conditions of the habitat at the various marshes, and provide the US Navy with a perspective on the relative importance of the populations occurring on Navy-owned land.
11	U.S. Fish and Wildlife Service. 1991. A survey of the Belding's savannah sparrow in California, 1991. Report to the California Department of Fish and Game. 24 pp. and survey site maps.
	Report on a survey for territorial Belding's savannah sparrow at 34 marshes between southern Santa Barbara county and the border with Mexico. Results are discussed within the context of previous years' data and recommendations are provided for further study and habitat improvements. The survey was carried out to provide an update on population data and to evaluate habitat conditions.
12	Boyer, Dave. US Marine Corps Base, Camp Pendleton. Personal communication, December 8, 1995.
13	MEC. 1993. San Dieguito Lagoon restoration project regional coastal lagoon resources summary. 56 pp plus an appendix.
	This report provides a summary of habitat types, fish, bird and benthic invertebrate populations at 16 coastal wetlands south of Anaheim Bay. It is a synopsis of primarily existing information; sources used in identifying and quantifying habitat types include aerial photographs taken in early 1993. Discusses restoration of habitats at San Dieguito Lagoon given present and historic conditions of other coastal wetlands in the region. This report was prepared as part of the San Dieguito Restoration Project undertaken by Southern California Edison to mitigate for damage to coastal marine resources from the operation of the San Onofore Nuclear Generating Station.
14	California Coastal Conservancy. 1995. Santa Margarita River Watershed Enhancement Plan Work Plan. 15 pp.
	The Work Plan details the purpose and goal of the Santa Margarita Watershed Enhancement Plan and outlines the scope of work for the project. Approximate cost and schedule information is included.
15	San Marino Environmental Associates. 1994. The status and distribution of the tidewater goby, Eucyclogobious newberryi (Pisces, gobiidae), on MCB Camp Pendleton, California. 59 pp and detailed field notes.
	Report of a survey of 8 lagoons on US Marine Corps Camp Pendleton to augment data on population fluctuations, abundance and habitat conditions of the tidewater goby, a federally-listed endangered species.
	Includes discussion of habitat conditions and recommendations for managing habitat to ensure survival of the species. Maps of station locations are included as well as field notes on each haul.
16	Odermatt, John R. and John P. Anderson. 1994. Water resources and pollution prevention in the Santa Margarita River Basin at the U.S. Marine Corps Base, Camp Pendleton, California. Pages 57-74 in Phillip S. Rosenberg ed. Geology and natural history: Camp Pendleton United States Marine Corps Base, San Diego County, California.
	This paper reviews existing information on geology and water resources in the Santa Margarita watershed, identifies environmental conditions and on-base activities that may affect water quality long-term and makes recommendations or protecting water resources within portions of the watershed on Camp Pendleton. The analysis includes assessment of ground water supplies and contaminant transport within sub-basins of the watershed.
17	Caspars, J. L. US Marine Corps Base, Camp Pendleton. Personal communication. May 13, 1996.
18	Zembal, Richard. 1995. Status and distribution of light-footed clapper rails in California, 1980-1995. Preliminary report to the California Department of Fish and Game. 28pp.
	Results of the 1995 survey of breeding light-footed clapper rails in California. The report incorporates data from 15 years of annual surveys and discusses population trends for the region and at each of 36 sites censused. Trends are tied to ecological conditions at each site and the author identifies possibilities for improving habitat.
19	Foster, Brian D. 1996. Breeding status of the California least tern at Marine Corps Base, Camp Pendleton, CA 1995. Unpublished report prepared for the Natural Resources Management Branch, Southwestern Division Naval Facilities Engineering Command, San Diego, California. 132 pp.
	Reports results of Ca least tern monitoring during the breeding season, April-August 1995 at 5 sites near the mouths of Aliso and French Creeks and the Santa Margarita River. Data on nest distribution, abundance and chronology, mortality, predation, reproductive success and fledgling production are presented. Methods included banding. Appendices contain: photos of nesting areas and notable features and plants species lists; descriptions of basic habitat conditions at each site as part of an evalution of the need for vegetation suppression; banding data sheets; National Wildlife Health Center necropsy reports; field notes, fledgling count data by site; and observations of banded snowy plovers.
20	Mudie, Peta J. 1969. A survey of the coastal wetland vegetation of North San Diego County. California Department of Fish and Game.18 pp. and appendices.
	Reports results of a survey of wetland vegetation at Santa Margarita, Las Flores, and San Mateo estuaries conducted as part of enhancement plan development. Analysis includes a description of plant community composition and structures, and characterization of soil types, moisture and salinities. Recommendations for habitat management take into account conditions at other San Diego coastal salt marshes.
	Appendices contain vegetation maps, stream flow data, transect results, and plant checklists for each site.

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