San Elijo Lagoon

GENERAL			Source
Site	San Elijo Lagoon
Map	Encinitas USGS 7.5' quadrangle.
Location	20 miles north of the City of San Diego, between the cities of Solana Beach and Encinitas.
Contacts	San Diego Parks and Recreation, 619-694-3047
	California Department of Fish and Game, 619-467-4202
	San Elijo Lagoon Conservancy, 619-436-3944
Approximate Wetland Habitat Acreage	576		13
Approximate Historic Acreage	415 acres of low marsh		13

Ownership in acres	Owner	Acres	Source
	Department of Fish and Game	349	14
	San Diego County	142	14
	San Elijo Lagoon Foundation and private	Not available	9
	State Lands Commission	372	14

LAND USE			Source
Land Use Designation	Ecological reserve/open space/parks in the Encinitas General Plan.		1
Onsite Use	Highway 101, the Santa Fe Railroad, and I-5 divide the lagoon into three basins connected by narrow channels. The San Diego County, with the assistance of the Dept. of Fish and Game (DFG), manages all three basins as an Ecological Reserve.		1
	The Reserve has 10 miles of trails and accommodates about 50,000 visitor-days per year; most use is passive recreational; fishing and horseback riding are permitted in selected areas.
Historic Use	Several dikes and levees were constructed between 1880 and 1940 to create access roads, duck ponds, and sewage treatment ponds. The dikes have eroded and hunting was discontinued		1
	in 1971. From 1940 until as late as 1973, the lagoon received wastewater from the City of Escondido.
Near Use	The City of Encinitas lies to the north of the lagoon. The City of Solana Beach bounds the southern side of the lagoon. To the west is Highway 101 and a small area of privately owned businesses. A developed unincorporated area of		1
	San Diego County lies to the east. Two state beaches occupy the areas directly north and south of the lagoon mouth. Surrounding uses include residential development, agricultural and recreation.
Historic Near Use	Agriculture		1

HYDROLOGY			Source
Tidal Influence	Highway 101, the railroad, I-5, and the east basin flood control dike limit the reach of tidal action. The lagoon is connected to the ocean via a narrow rip-rapped channel. Once fully tidal, the tidal prism is currently insufficient to maintain an open		1, 3, 8, 5, 15-17, 19
	ocean inlet. The potential mean tidal prism is 105 ac.-ft, the mouth was open 24% of the time from April 1991 through February 1994. Mechanical clearing of the inlet helped keep it open for 4 months in 1994 and 10 months in 1995.
Watershed Area	77 Square Miles		1

Tributaries and Flow	Tributary	Flow	Source
	Escondido Creek	Formerly ephemeral, the creek now flows year round due to drainage of water brought in to the watershed for urban uses; based on information from 1961 and 1972 the estimated 100-yr peak flow at the lagoon was 22,000 cfs;	3
		the creek is contained by a concrete channel through the City of Escondido.
	La Orilla Creek	Not specified	1
Dams	Lake Wohlford constructed in 1924 as well as Dixon Lake in the Escondido Creek drainage, and San Dieguito Reservoir in the La Orilla Creek Drainage.		3
Other Sources	Not specified		3

WATER QUALITY			Source
General	Current problems include fluctuating salinity levels, eutrophication, high levels of bacteria, accelerated sedimentation and excess freshwater. Listed in 1994 as an impaired water body; draft 1996 list indicates		3, 10, 11, 12
	selected criteria for eutrophication, sediment and coliforma bacteria exceeded. Beneficial uses are rec1, rec2, biol, est, wild, rare, mar and migr.
Dissolved Oxygen (DO)	Data were collected from spring 1993 through winter 1994, data summarized below are from the east and west basins. A.M. readings of bottom water recorded a range of approximately 0 to 15 mg/l between March 1993		1, 7
	and Feb. 1994 (mouth mostly closed), and 1 to 9 mg/l between March and July 1994 (mouth mostly open). Temperature was measured but not reported. Concentrations below 4 mg/l occurred in June-August, and October 1993 and July.
Water Salinity	Data were collected from spring 1993 through winter 1994, data summarized below are from the east and west basins. Between March 1993 and Feb. 1994 (mouth mostly closed), the salinity levels for both basins ranged from about 1 to 33 ppt.		7, 8
	Between March 1993 and July 1994 (mouth mostly open) the salinity range was about 2 to 30 ppt; within each period salinities were observed to be low when the mouth was closed and high when the mouth was open.
Sediment	The Soil Conservation Service estimated in 1993 that the total sediment delivered to the lagoon is about 30,000 tons per year. The average annual sedimentation rate was estimated at 0.3 inches/year.		1

Soil			Source
Soil	16-26 feet of organic silty clays overlay about 130 feet of fine to coarse sandy silts.		1

Habitat	Acres	Vegetation
Open Water Estuarine and fresh	148	1993-1994 Ditch grass and Enteromorpha sp. occasionally found in tidal channels throughout the monitoring period.	Ac.13, Plants 7
Sand/mud flats	109	1993-1994 Ditch grass, pondweed, water nymph and <i>chara vulgaris<i>, fresh lake species, were very abundant forming a dense stand in summer 93 (mouth closed); a smaller stand of Enteromorpha developed in summer '94 (mouth open).	Ac.13, Plants 7
Coastal Salt Marsh	78	1993 - pickleweed, fleshy jaumea, alkali-heath, saltgrass, alkali weed, salt marsh daisy, and shoregrass were dominant. No cordgrass.	Ac. 13, Plants 18
Fresh/brackish Marsh	213	1993 - Cattail, alkali bulrush and California bulrush were dominant.	Ac. 13, Plants 18
Riparian	28	1995 report - Habitat characterized as a few pockets of riparian species.	Ac. 13, Plants 1
Upland	300	1995 report - western dichondra+, San Diego barrel cactus+, Del Mar Mesa sand aster+, Nuttall's lotus+ present in chaparral, coastal sage scrub or coastal strand communities.	1

ANIMAL USE			Source
Birds	1994 -130 species identified during monthly surveys, 76 water-associated including 13 sensitive; 10 sensitive upland species; light-footed clapper rail#, California least tern#, western snowy plover#, and Belding's Savannah sparrow# nesting 1986-1993.		1, 2
Fish	1992-1993 - 10 species were caught in seines and traps during summer (mouth closed), Topsmelt was most abundant by far, other species included northern anchovy and yellowfin goby*. 4 species caught in winter (mouth open), with numbers very reduced.		5
Benthic Invertebrates	1992-1993 - 12 species were collected from cores at four sites; Orchestia traskiana, an amphipod, and Polydora nuchalis, a polychaete, were the most abundant species; crayfish, shrimp and crabs were also caught in fish traps.		1, 5
Insect	1989-1990 - 16 orders of arthropod including the Saltmarsh wandering skipper+, were found in 4 wetland habitats and chaparral scrub; ants, bees, wasps, flies, beetles, amphipods, and isopods were most abundant.		1
Other Wildlife	1979-1991 - 26 native and 3 naturalized mammal species including mountain lion, coyote, bobcat, fox, and racoon over all habitats; 16 native and 3 naturalized reptile and amphibian species including the two-striped garter snake in central and east basins.		1
Special Status Species	1979-1994 - San Diego marsh elder+, and 3 other plant species in upland areas; Common loon, Amer white and Ca brown pelicans+, double-crested cormorant, white-faced ibis, light-footed clapper rail#, western snowy plover#,		1, 2
	long-billed curlew, Ca gull, Ca least tern#, elegant tern, North harrier, sharp-shinned hawk, Cooper's hawk, Osprey, Belding's Savannah sparrow# and 12 other sensitive bird species nesting in upland areas, including the California gnatcatcher+;
	Salt Marsh wandering skipper+; 2 reptile species documented in uplands; 3 upland mammal species.

OUTLOOK			Source
Enhancement Status	A draft Enhancement Plan was prepared by the County in August, 1995 to recommend methods to preserve and augment a gradient of self-sustaining habitats that range from salt marsh to freshwater marsh. San Diego County		1
	manages the lagoon and when funding is available coordinates the opening of the mouth; there have been 16 artificial openings between 1986-90. An experimental removal of the sand/cobble berm at the mouth kept the inlet open from 4/20 - 8/23, 1994.
	The mouth was manually opened again in June 1995. Biological monitoring is carried out before and after mouth openings.
Watershed Management	1993-Soil Conservation Service prepared the Escondido Creek Hydrologic Area report. It presented four alternative management schemes for reducing erosion and sedimentation. No new programs have been implemented as of October 1995.		3, 9
Pressure	Lack of funding to maintain an open lagoon mouth; sedimentation; agriculture, fires and urban development in watershed; exotic vegetation and fauna; off-road vehicle activity; and increased visitor usage.		5, 9

Comments
SOURCES
1	County of San Diego Parks and Recreation. 1995. Draft San Elijo lagoon area enhancement plan. 110 pp. and appendices.
	The plan recommends methods to preserve and augment a gradient of self-sustaining habitats at the lagoon. It covers existing conditions, including geology, hydrology, and biological resources. Opportunities and consraints for lagoon enhancement are
	discussed. The appendices include original fieldwork and analyses conducted for hydrology, water quality, fish and invertebrates.
2	San Diego Audubon Society. 1995. San Elijo lagoon bird census for 1990 - 1995. Freeman F. Hall count leader. Unpublished survey data. 8 pp.
	Summary of monthly survey data collected by the San Diego Audubon Society at San Elijo lagoon from 1990 -August 1995.
3	USDA Soil Conservation Service. 1993. Escondido Creek hydrologic area project report. 174 pp. and appendices.
	The San Diego Regional Water Quality Control Board contracted with the USDA Soil Conservation Service to develop a Nonpoint Source Pollution Management Plan for San Elijo Lagoon and the Escondido Creek Hydrologic Area. This report fulfills part of the
	contract. It discusses water quality problems in the watershed and provides detailed analyses by subwatershed of current and future land uses and associated sediment, nutrient, and freshwater inputs. Incorporates existing information.
4	Welker, Susan and Robert Patton. 1993. San Elijo ecological reserve biological element for master plan/management plan. Draft. Prepared for the County of San Diego Parks and Recreation Department. 128 pp.
	The report addresses the biological aspects of the San Elijo Lagoon Ecological Reserve. It compiles all available biological data on the area. Incorporates data from various surveys conducted between 1973 and 1993 on vegetation, birds, mammals,
	water quality, fish and invertebrates.
5	Boland, John, Pacific Estuarine Research Laboratory (PERL) for the San Diego County Department of Parks and Recreation. 1993. The physical, chemical and biological monitoring of San Elijo lagoon, final annual report. 16 pp.
	Reports results of water quality, benthic invertebrate, and fish sampling carried out at San Elijo Lagoon February 1992-February 1993 as part of an ongoing monitoring program. Discussion includes comparisons both to previous years' data and to
	water quality conditions at Los Penasquitos Lagoon.
6	Elwany, M. Hany S, Alan Thum, Reinhard E. Flick, Saima Aijaz, and Doug Gibson. San Elijo Lagoon monitoring before and after June 1995 inlet excavation. 1995. Prepared for the San Elijo Lagoon Conservancy. 14 pp.
	This report documents the changes in inlet topography within 30 days of the June 1995 inlet excavation at San Elijo Lagoon. Elevations were measured at 12 sections across and along the inlet channel, the adjacent beach and east of Highway 101
	before and after dredging. Includes descriptions of excavation and survey methods and figures showing the cross-sectional profiles.
7	Boland, John M. 1994. Water quality at San Elijo lagoon 1993-1994: Section III Oxygen depletion and nutrient availability. Pacific Estuarine Research Laboratory (PERL), for San Diego County Department of Parks and Recreation. 83 pp.
	From February 1993 to July 1994 nutrient, plant abundance, dissolved oxygen and salinity data were collected to learn about the connection between these parameters and eutrophication at San Elijo Lagoon. Monitoring spanned the April 1994 experimental
	opening of the ocean inlet and data for each year are presented seperately. Results are discussed relative to whether the mouth was open or closed.
8	Boland, John M. and Hany Elwany for the California Coastal Commission and San Elijo Lagoon Conservancy. 1994. Sand and cobble removal from the mouth of San Elijo lagoon. First, second, and final reports. 3 to 6 pp., plus attachments.
	These reports, prepared to comply with a Coastal Commission permit condition, report data collected during and after an experimental excavation of the sand/cobble berm at the lagoon mouth. The mouth stayed open from April 20 to August 23rd.
	The shape of the inlet channel, tidal ranges, water level ranges, coliform bacteria, salinity, and dissolved oxygen were measured March through July, 1994 to evaluate effects on lagoon resources and public recreation.
9	Barbara Simmons, San Diego County Department of Parks and Recreation. Personal communication October 13, 1995.
10	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.
11	State Water Resources Control Board. 1994. List of impaired water bodies.
	Developed as part of the Water Quality Assessment of the State's major waterbodies. Separate lists are developed to rate waterbodies as Good, Intermediate, Impaired or Unknown Quality. Impaired waters are those not expected to attain or maintain
	water quality standards. The state list is a compilation of those developed by the nine regional boards. Lists of impaired water bodies are also known as 303(d) lists as they meet a requirement of section 303(d) of the federal Clean Water Act.
12	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.
13	MEC. 1993. San Dieguito Lagoon restoration project regional coastal lagoon resources summary. 56 pp and 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 Department of Fish and Game. 1995. Real property inventory: comprehensive parcel list by name.
15	Boland, John. 1992. The physical, chemical and biological monitoring of San Elijo lagoon, final annual report. Pacific Estuarine Research Laboratory (PERL) for the San Diego County Department of Parks and Recreation. 21 pp.
	Reports results of water quality, benthic invertebrate, and fish sampling carried out at San Elijo Lagoon April 1991 - February 1992 as part of an ongoing monitoring program. Discussion includes comparisons both to previous
	years' data and to water quality conditions at Los Penasquitos Lagoon. Management recommendations are also provided.
16	Boland, John. 1994. The physical, chemical and biological monitoring of San Elijo lagoon, final annual report. Pacific Estuarine Research Laboratory (PERL) for the San Diego County Department of Parks and Recreation. 16 pp.
	Reports results of water quality, benthic invertebrate, and fish sampling carried out at San Elijo Lagoon February 1993 - February 1994 as part of an ongoing monitoring program. Discussion includes comparisons both to previous
	years' data and to water quality conditions at Los Penasquitos Lagoon. Management recommendations are also provided.
17	Boland, John. 1994a. The physical, chemical and biological monitoring of San Elijo lagoon, final report. Pacific Estuarine Research Laboratory (PERL) for the San Diego County Department of Parks and Recreation. 16 pp.
	Reports results of water quality, benthic invertebrate, and fish monitoring carried out at San Elijo Lagoon February 1993 - July 1994. Discussion includes comparisons to previous years' data and a summary of important
	findings derived from 5.5 years of monitoring. Management recommendations are also provided.
18	Boland, John. 1994b. The vegetation monitoring at San Elijo Lagoon during 1993. Pacific Estuarine Research Laboratory (PERL) for the San Diego County Department of Parks and Recreation. 9 pp. and appendix.
	Results of a vegetation and soil salinity survey conducted to establish baseline conditions. Percent cover was measured in April along 19 transects covering salt and brackish marsh areas; five of these had also been surveyed in 1990. Soil salinities were
	measured in April and September. Discussion includes analysis of spatial and temporal (for salinity) variations and comparisons to vegetation distributions at Los Penasquitos Lagoon. Appendices contain photographs of each transect along with
	associated results for soil salinity and percent cover.
19	Elwany, Hany, Alan Thum, Saima Aijaz, and Linda Holmes Dean. 1995. 1995 inlet channel excavation and maintenance efforts at San Elijo Lagoon. 67 pp.
	This report describes inlet dredging operations undertaken in June and December 1995 and presents results of topographic and hydrological monitoring carried out between May and November 1995. Results are provided for 4 topographical surveys
	and continuous water level measurements of the inlet. Analysis includes correlations of these data with tidal and wave conditions and freshwater input before and after dredging, as well as with results from 1994 studies. A brief summary of concurrent
	water quality and biological monitoring data is also provided along with recommendations for future work to support an inlet and biological management plan for the lagoon.

Webmaster: wetlands@resources.ca.gov

Webmaster: wetlands@resources.ca.gov