Native groups representing the San Dieguito, La Jolla, and Diegueno Indians occupied the San Elijo Lagoon area from 10,000 years before present to the historic period. The activities of their cultures had a minor impact on the hydrological, geomorphic, and biological evolution of the lagoon. The hunting and gathering lifestyle of the resident people probably reduced populations of some plant and animal species, and may have fostered others. It is likely that brush fires played a role in the vegetational mosaic of the area, as native peoples are known to have actively managed vegetation for game and certain food plants.
San Elijo Lagoon was given its name in 1769 by the Portola
Expedition on its way to Monterey. Spaniards and other Europeans settled in the
region and established cattle ranches in the early 1800's, and the population
grew rapidly after 1848 with the discovery of gold in California. Early
permanent Anglo settlements were established in the 1880s. The community of
Olivenhain on Escondido Creek, established as an experimental farming community,
was in influential force in the area. This marked the start of a period of
radical vegetation shifts and land conversion. Riparian areas seem to have been
especially modified. During this time, cultivation of sandy coastal soils
encouraged the replacement of native bunch grasses with non-native, annual
species.
After the 1880s, human modifications to the hydrological
system of San Elijo lagoon and watershed accelerated at a rapid pace. Several
dikes and levees were constructed between 1880 and 1940 to create access roads,
duck ponds, salt harvesting ponds and sewage treatment ponds. The partitioning
of the lagoon and restricted tidal action altered natural flow paths, and led to
an accelerated rate of sediment deposition, and subsequent impairment of the
water quality of the lagoon. A berm and bridge crossing near the mouth of the
lagoon was completed in 1887 to support installation of the Santa Fe Railroad.
This construction reduced the connection between the lagoon and ocean to a
narrow channel. The inlet channel was further confined to the northern end of
the beach in 1891 with the construction of a plank road, the present day Highway
101, build on what would have been barrier dunes along the ocean. The present
day SDNR bridge was constructed in 1925, reducing the inlet channel width from
approximately 500 to 250 feet. The existing bridge for Highway 101 was completed
in 1932, further confining the inlet channel. In 1934, more fill was added to
support the railroad. In 1965, Interstate 5 was constructed, dividing the
wetland area in half. In 1981, the California Department of Fish and Game and
the County of San Diego built the east basin water management project to
manipulate water levels for flood and mosquito control. The project included
restoration of a dike, and installation of water control gates, two concrete
spillways and a pond with two Least Tern nesting islands. In 1945, the elevation
of Manchester Avenue was raised to reduce the flood frequency on the road. Prior
to 1985, the lagoon was artificially opened mainly to allow Manchester Ave. to
remain passable during times of high water.
Natural freshwater inflows to the lagoon were reduced to
ephemeral surface flows as a result of the construction of reservoirs on
Escondido creek. The dam for the largest reservoir in the watershed, Lake
Wohlford, was completed in 1924. During this period, the east basin was diked to
control flow and became a salt flat where salt was harvested from sea water
captured on the high tide. Between 1940 and 1973, wastewater was discharged from
local sewage treatment plants into Escondido Creek and the lagoon itself,
causing a shift in the lagoon from saltwater habitat to a more brackish system.
Cardiff and Solana Beach sewage
treatment plants discharged into the lagoon from
1940 until 1966, after which the wastewater was discharged through an outfall
into the Pacific Ocean. Between 1959 and 1973, the City of Escondido discharged
treated wastewater into Escondido Creek at the rate of 3.5 million gallons per day (mgd). Estimates are that approximately 2.5 mgd reached the east basin as
surface flow. This treated effluent was diverted into ponds in the lagoon to
provide further treatment, waterfowl habitat, and hunting opportunities. These
dikes have eroded gradually, and in 1971 official hunting was discontinued in
the lagoon. In 1973, the County of San Diego upgraded the wastewater facilities.
Currently, the treated wastewater from Solana Beach, Cardiff and Escondido is
discharged through San Elijo outfall to a distance approximately 1.5 miles
offshore. The San Elijo outfall is managed by the San Elijo JPA consisting of
the Cardiff and Solana Beach Sanitation Districts.