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Abrupt Late Holocene Closure of San Elijo Lagoon, Northern San Diego County, California

Department of Geological Sciences, California State University of Fullerton, Fullerton, CA 92834, USA
Author to whom correspondence should be addressed.
Coasts 2023, 3(3), 227-239;
Submission received: 24 May 2023 / Revised: 22 August 2023 / Accepted: 29 August 2023 / Published: 30 August 2023


The San Elijo Lagoon experienced a sudden shift in sedimentation type around 1000 AD, as evidenced by the 14C dating. This shift is marked by a sharp boundary between a lower layer of medium to fine sand and an upper layer of dark, silty clay that reflects the lagoon closure. The dated sediments also reveal a history of marine conditions in the lagoon basin since about 7400 ± 140 years before the present (ybp), when the sea level was −12.2 meters (m), and the shoreline was 400 m away from the current location. The sea level rose at a rate of 2.84 m per 1000 years until about 4170 ± 100 ybp. After that, the rising sea level slowed and reached the present level about 3100 years ago. However, the lagoon remained closed after about 730 to 1180 ybp, with only fine organic sediment accumulating in the basin, which coincides with a severe drought in the southwest around 1150 AD. A higher sedimentation rate is interpreted from bluff erosion as seen after 520 ± 40 ybp but without enough stream flow to force the reopening of the lagoon.

1. Introduction

Tidal inlets along the southern California coast have evolved. Climate change, sea-level fluctuations, tectonic movement, sediment load, and shoreline processes played a prominent role in the evolution of San Elijo Lagoon [1,2] (Figure 1). The San Elijo Enhancement Plan [3] proposes the deepening and widening of the existing lagoon’s tidal channel system [4]. Fine-grained sediments form a surface layer overlying the lagoon channels and intertidal mudflats. This study evaluated these upper sediments via grain size characterization, mineralogical, and carbon dating. Sample location sites were chosen to provide coverage of the lagoon while avoiding sensitive habitats and reworked areas.

1.1. Background

Earlier research in the lagoon has focused entirely on deep sediments or offshore geotechnical work [5,6,7,8,9]. Work on other nearby coastal lagoons has included marine terraces [10,11,12,13,14], coastal flooding [7,15], sea-level rise and fall [16,17], as well as tectonic uplift and movement along the shoreline [12,18]. Earlier research in the back of the lagoon focused on four deep-cored boreholes excavated in the area east of Interstate 5 [7,8]. The deepest of these cores was 18 meters (m) and recovered from where Escondido Creek enters the northeasternmost part of the lagoon (Figure 2).
The earlier information was augmented during this investigation with an added 45 sediment cores recovered manually from the lagoonal area west of Interstate 5 (Figure 2). These new cores were used to find the overall thickness of the fine-grained organic-rich material that overlays the coarser sands below [19]. As a result of the sediments collected, the age dates of lagoon sediments were used to find the age of the first lagoon closure as identified by the change from a uniform substrate of sand to the upper approximant meter of organic mud [20,21].

1.1.1. General Setting

San Elijo Lagoon is a coastal wetland in the San Elijo Lagoon Ecological Reserve, San Diego County. The lagoon is approximately 32 kilometers (km) north of San Diego and extends inland about 4 km with a width of about 0.4 to 1.2 km. Escondido Creek and La Orilla Creek enter the lagoon at the eastern end. San Elijo Lagoon is one of six coastal lagoons formed at the distal end of westward draining creeks, streams, and rivers cutting through the marine terraces of northern San Diego County.
San Elijo Lagoon is separated into three distinct basins, east, central, and west, connected by narrow channels confined by the freeway, highway, and railroad north-to-south crossings. Prior studies have collected geological, paleontological, and archaeological data from various parts of the basins as well as the surrounding bluffs, and a deep investigative well has been placed in the central portion of the lagoon on the northern flank of Interstate 5 by the U.S. Geological Survey. This study is confined to our investigation of the Central basin between Interstate 5 and the right of way for the Amtrak, Santa Fe, and San Diego Coaster railroad track bed and elevated trestles, and the West basin, which is much smaller and confined between the railroad and Highway 101, west of which is the shoreline.
The lagoon consists of channels, salt marshes, mudflats, and wetlands that are both brackish and freshwater, totaling approximately 239 Hectares. The western basin comprises four to five inter-connected tidal ponds totaling 18 Hectares; the central basin constitutes 89 Hectares of mudflats and shallow open water, and the eastern basin is approximately 104 Hectares of shallow fresh and brackish wetlands.

1.1.2. Geologic Setting

The coastal zone of northern San Diego County is characterized by a 100 m high, very straight bluff interrupted by lagoons forming in the filled valleys of westward draining streams [22]. San Elijo Lagoon is one of several lagoons that form these drowned mouths of coastal streams. San Elijo Lagoon is fed by the Escondido Creek watershed, which includes about 600 km2 of the mountainous and coastal plain zones of northern San Diego County.
The Eocene Torrey Sandstone and Delmar Formation (interbedded sandstone, siltstone, and claystone) are exposed in the bluffs around the lagoon, and Cretaceous age coarse sediments of the Lusardi Formation underlie these formations and are exposed east and southeast of the lagoon in Rancho Santa Fe [23]. Pleistocene terrace deposits of sand and silt overly the Eocene rocks and form a relatively level surface on the bluffs. The lagoon is composed of alluvial and lagoonal deposits, as well as sediments of a once-open marine embayment. These unconsolidated sediments are up to 30 m thick and are mostly thick sections of marine sands and sandy clays with rare layers or lenses of gravel and cobbles.
Several periods of glaciation have caused sea levels to fluctuate worldwide by as much as 122 to 152 m [16,17,24], with the most recent period of glaciation ending at approximately 20,000 years before present (ybp). Numerous marine terraces have been identified along the coastline from Baja California to the Monterey Peninsula that represent cycles of bluff retreat and subsequent deposition onto the eroded platforms and, combined with the local tectonic uplift of the California coastline, have created an inward stairstep of terrace risers and treads along the coast [10,11,12,13]. At least nine marine terraces, trending nearly parallel to the present-day shoreline, are preserved along this stretch of coast [10].
San Elijo Lagoon is a wetland overlying sediments deposited during the deglaciation of the past 20,000 years [25,26]. The lagoon currently maintains contact with the ocean through a natural, although artificially maintained, inlet at its northwest corner (Figure 2). During the mid to late Holocene, the lagoon existed as a deep open bay and, prior to the most recent deglaciation, was a deeply cut river basin extending to the edge of the continental shelf [27]. During the Quaternary Period, the coastal area of northern San Diego County has been undergoing an uplift of about 0.13 to 0.14 millimeters per year (mm/yr) [11,12,28]. However, new dates of the marine terraces reveal a revised estimated rate of coastal uplift of 0.066 +/−0.020 mm/yr [12,28]. The date of formation of the oldest terrace is believed to be 800,000 ybp, while the youngest terrace is believed to have formed somewhere around 85,000 ybp [10,11,29].

2. Methods

2.1. Sample Collection

Sediment was collected from 45 locations throughout the central and western basins of San Elijo Lagoon, west of the Interstate 5 Highway (Figure 2). The locations were chosen to be representative of the surficial 1 m of soil from various parts of the lagoon. Each site was surveyed using both global positioning systems (GPS) and conventional land surveying techniques (electronic total station) (Leica TC905L). The samples were collected by driving a steel sampling pipe (macro-core from Geoprobe®, Salina, KS, USA) fitted with clear PVC sleeves into the soft lagoonal soils to a depth of approximately 1 m. The macro-core sampling sleeves were 91 centimeters (cm) long and 5 cm in diameter. Once the sampler was driven into the lagoonal soils and brought back to the shore, the inner core sleeve was removed and cut in half lengthwise. Half of each sample core was archived in aluminum foil, labeled, cataloged, and stored in the laboratory. At the same time, the other half was described using the Unified Soil Classification System (USCS) for soil type, group symbol, plasticity, moisture, and density. Color variations were also described to visually characterize the organic content.
Each sample core was air-dried for further analysis. Grain size analysis was run on 10 of the 45 core samples collected. The following sampling locations were chosen for this first grain size analysis (Samples 111, 116a, 116b, 119, 124a, 124b, 131, 133, 136, and 145). These sample cores were chosen based on their variability in location throughout the lagoon but also because they contained a significant coarse fraction based on visual analysis. Only non-organic sediments greater than approximately 1 mm were selected for grain-size analysis. The selected samples with initial masses between 50 and 80 grams (g) were oven-dried at 44.5 °C for 24 hours to ensure that all moisture in the samples had evaporated. The sediment samples were weighed and sieved using three different sieve nests at 0.5 Φ intervals from −0.5 Φ (1.40 mm) to 4.5 Φ (0.045 mm) in a Ro-Tap™ shaker for twenty minutes each. The fractions held within each screen were then weighed. The data were then plotted on cumulative probability curves, which were used to provide percentile parameters for the statistical determination of the mean and median and the sorting of the samples. Size frequency histograms were also constructed. The histograms were then used to find the mode and modal class (Figure 3).

2.2. Radiocarbon Analysis

Eight samples (including plant fragments and samples with high organic content) from various locations and depths within the lagoon were chosen for radiocarbon analysis (Figure 4). The selected samples were then sent to Beta Analytic Inc. (Miami, Florida) for analysis. All samples were analyzed using the accelerator mass spectrometry (AMS) method. AMS uses a particle accelerator to achieve energies high enough to measure individual 14C ions. This method allows for the analyses of smaller sample sizes while supplying the high-precision results obtained in the best traditional laboratories [30,31]. The results obtained from Beta Analytic are given in Table 1.
The 13C/12C was calculated by Beta Analytic Inc. laboratory to normalize the results to a δ13C value of −25‰ compared to the PDB-1 international standard. The ratio is also used to correct for isotopic fractionation effects. These corrections are then applied to the Measured Radiocarbon Ages (MRA) to calculate the Conventional Radiocarbon Ages (CRA).

3. Results

3.1. Sediment Analysis Results

A sediment-filled offshore channel cut through Eocene rock formations extends to the continental slope two miles offshore of San Elijo Lagoon. The talweg of the channel extends upstream below the lagoon to the juncture with La Orilla and Escondido Creeks in the eastern basin area of the lagoon, where it emerges from being below the bay sediments of the lagoon into the fluvial deposits of the creeks. The lagoon sediment is composed of marine sands and silts that date from about 7400 ybp at a depth of 15 m. Bay sediments extend to the coastline, where they are buttressed by a shoreline berm of sand 4 m above sea level. Offshore of the berm, the seabed consists of exposed eroded bedrock and channelized sediments.
An isopach (thickness) map shows the thickness variation of the organic-rich upper layer overlying the silty sand in Figure 5. This fine-grained upper unit was found to vary in thickness from 5 to 100 cm. The lagoon elevation minus the depth to sand elevation gives an organic-rich layer thickness of 0.9 m on average over the entire lagoon area. The thinnest amount of organic-rich sediment is present in the western basin, and the central basin mudflats are the thickest. At some locations, this layer has been subject to scouring during flooding; at others, it is formed of evenly layered deposits.
The entire soft sediment deposit was sampled down to a compacted mud or hard silty-sand layer in the mud flats and the main channel bed. The thickness ranges from a high of 1.1 m in the central basin center mudflat area to a low of 0.3 m in the southern part of the western basin. The mudflat site averages an elevation of 0.54 m above mean sea level, while the silty sand layer below it has an average elevation of −0.37 m below the mean sea level. The organic soil composition includes palynological material, including pollen spores of oaks, pines, chaparral, and other common shrubs, as well as fern and fungus, wood fragments, micropaleo (ostracodes and benthonic foraminifera, and megafaunal shells of intertidal mollusks, particularly Argopecten aequisulcatus, Chione sp., Ostrea lurida, and Tagelus californicus [32].
The samples collected from the sand layer were generally classified as moderately well-sorted fine sand. Size frequency histograms were also constructed. The histograms were then used to find the mode and modal class. Soil is silty to very fine sand and organic sediment in the core’s upper portion (SM 116, 124, 133, and 136) and grades into very fine sand (SP 111, 116, 119, 124, 131, and 145) of approximately 0.2 mm in size (Figure 3).
The visible angularity of the individual grains suggests that the provenance was proximal to the depositional environment. This angularity of the grains also indicates that the depositional site was not a beach but probably a bay/estuary. The fine-grain size suggests that removal energy in the depositional environment was relatively low, and the moderate sorting indicates that the energy in the depositional environment was constant, whereas modern beach sands are very well sorted and have grains that are angular to sub-rounded.

3.2. Radiocarbon Results

Organic soil/shells/wood samples were sent to Beta Analytic Inc. for radiocarbon analysis. Samples were analyzed using the conventional Decay Counting Method (DCM). This method involves measuring the activity of 14C by detection of β-decays. The results of the radiocarbon analyses are shown in Figure 3 and Table 1 and offer a range of ages in the upper soft organic zone from 1950 to 20 ybp. Radiocarbon samples were taken from the eastern basin during a study by [7,8] (Table 2). Samples were collected from two previous sampling locations, BH-3 and BH-4. All samples collected during this previous study were taken from depths much greater (down to 23 m below the land surface) than those taken in this study (maximum depth of 1 m).
Marine shells were found in the cores drilled by [7] at the very eastern end of San Elijo Lagoon, 2 km inland at an elevation of −12.2 m. The shells were found just below the organic soil, dated at 7100 ± 110 ybp, along with wood at 7400 ± 140 ybp. Detailed paleoenvironmental work by Pope et al. (2004) [9] reports dates of 7741 ± 78 and 7595 ± 45 ybp at similar depths from their boring SE-3 in the middle reach of the lagoon.

4. Discussion

According to Masters (1992) [25], sea level rose rapidly from about 20,000 ybp to around 6000 ybp at a 10 mm/yr rate. The coastal uplift rate is 0.13 mm/yr (or less) and is two orders of magnitude below the sea level rise, and, thus, did not significantly impact the effects of sea level rise or sedimentation.
As rapid transgression occurred, the lagoon was an open bay with abundant fish and invertebrates [33]. A similar conclusion is reached for Bataquitos Lagoon and Buena Vista Lagoon (San Luis Rey River), north of the study area, as documented in the midden of the La Jolla occupation starting at about 8000 ybp according to Miller (1966) [33], Bull (1981) [6] and Masters (1992) [25]. An unobstructed opening to the ocean and low sedimentation would dominate such a bay.
The head of San Elijo Lagoon, Escondido Creek, and La Orilla Creek have deposited debris from the hinterlands that formed deltas and marshes. As sea level rise slowed, the sediment being brought to the embayment would have filled it in, and longshore transport would eventually have sealed off the lagoon at the coastline. However, salt marshes would continue to develop inside the berm. Climatic conditions also contribute to slowing sedimentation, as the stream’s rainfall runoff would gradually decrease as the climate warms. Thus, fewer and less frequent storms would occur to flush the lagoon channel and keep the inlet open. Later, infilling and salt marsh expansion would occur. Once the lagoon closed, estimated by 14C ages from the soil above the bay sands to be about 3000 ybp, the fish and shellfish of the now closing embayment would disappear, and the thriving Indian occupation would begin to diminish. Such conditions are documented by the absence of midden sites after 3000 ybp until about 1000 ybp [6].
The variation in organic-rich sediment is tied to the location of the channel areas. As the channel enters the central basin area from the eastern basin (under I-5), the sediments are thin and thicken with downstream distance (Figure 4). The organic-rich deposit thins towards the lagoon outlet as it approaches Interstate 101. This is most likely caused by the active flushing of ocean water in this area, allowing less of a buildup of organic-rich sediment. The sediment is most likely derived from erosion for the exposed marine sandstone bluffs upstream and adjacent to the lagoon. The deposition rate shows a marked decrease in the younger age core sediments with a high of 2.84 m per 1000 years for the sediment deposited before 3340 ybp and 0.93 m per 1000 years for those deposited following 3340 ybp.
We dated sediments from the lagoon to record a history of marine conditions within the lagoon basin beginning at approximately 7400 ± 140 ybp at an elevation of −12.2 m. The shoreline at this time would have been 400 m offshore of the current strandline. The results of the sediment dates define a sea level rise of 2.84 m per 1000 years from 7400 ± 140 to 4170 ± 100 ybp tempered by a coastal uplift rate of 0.066 m per 1000 years. A general slowing of sea level rise is shown for the period following 4170 ybp. Rising at 2.84 m per 1000 years, the arrival of the shoreline at its present level occurred at 3105 ybp. However, per our data, the closure of the lagoon was permanent at about 800 to 1050 ybp, with only fine organic sediment accumulated in the basin after this period. Pope et al. (2004) [9] also note a restricted access basin between 300 BC and 1400 AD. This age is consistent with the initiation of significant drought in the southwest around 1150 AD, when even the major rivers may have dried up. An increase in sedimentation rates from bluff erosion is apparent following 800 ybp, though the associated stream flow was insufficient to establish a reopening of the lagoon. We consider this period to be consistent with the Little Ice Age from 1350 AD to 1870 AD.
Our results show that the lagoon’s sediments are sharply divided into an upper 0.6 to just over 1 m deep zone of soft clayey organic silt that overlies a substrate of firm, silty fine sand that is mostly non-organic (Figure 4). The estimated age dates collected from the upper organic zone varied from 1950 (considered 1950) to 400 to 500 ybp. This was when a sustained outlet to the ocean became blocked (only restricted sedimentation occurred). Before that time, the lagoon was open and received diurnal tidal flows, which removed the finer-grained sediment. The ages recorded in the upper muck also show that the sediment is generally older than historical time (200 ybp).
The estimated ages correlate well with earlier and subsequent studies throughout the area and substantiate that the historical sedimentation rates for the lagoon are very slow [12,15]. With the closing-off of the mouth of the lagoon to daily and seasonal tidal influences, the active flushing of the lagoon sediments has slowed down. The radiocarbon dates were used to assess the age of deposits, particularly since the earlier work in the area by Foster (1993) [7] showed ages in thousands of years for very shallow sediments. Results of the present study confirm this, with sediment at 40.6 to 61.0 cm being 500 to 1200 years old (estimates from before 1950).
There are inherent errors in age dating lagoonal sediments in an active area, including vertical or post-depositional modification mixing. Based on the sedimentological assessment, we saw little to no evidence of post-depositional modification of the sediments in the principal areas of our investigation. However, later analysis showed three age-dated locations impacted by construction, so we did not use the dates obtained from those locations. These are perimeter locations and do not change the results from the central lagoonal portion of the study area.

5. Conclusions

The central basin of San Elijo Lagoon has approximately one meter of grayish brown organic fine sandy silt overlying gray fine to medium sand throughout. A two- to three-meter-deep narrow channel has been cut into the dense sand with loose sand deposits along its course. The channel has remained within its current course since the earliest overflights, and maps record its location. The upper fine sediment cover is attributed to a closing of the lagoon at approximately 900 ybp based on the age dates of the organic-rich zones in the upper meter of soil. The closure of the lagoon is an event that predates the construction of railroad and automobile roadways across the lagoon. Its age suggests it coincided with a considerable drought period in the southwest and before or at the initiation of the Little Ice Age, but no actual causes are known. The channel opening is restricted to the lagoon’s north side, and the existing tidal prism is insufficient to keep the channel open. No evidence of recent flood deposits is present in any of the 45 core samples from the upper meter of sediment despite the historical record of large-scale flooding in San Diego from the 1916 and 1938 events.

Author Contributions

W.R.L.: Conceptualization, investigation, methodology, writing—original draft preparation, writing—review and editing, project administration. J.H.F.: Conceptualization, methodology, investigation, writing—original draft preparation and funding acquisition. All authors have read and agreed to the published version of the manuscript.


This research received funding from San Elijo Lagoon Conservancy.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Not applicable.


San Elijo Lagoon Conservancy—Doug Gibson. Students—Otto Figueroa, Sean Hunt, Rene Perez, and Kevin Voorhis.

Conflicts of Interest

The authors declare no conflict of interest.


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Figure 1. Index Map.
Figure 1. Index Map.
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Figure 2. Sample Locations.
Figure 2. Sample Locations.
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Figure 3. Grain size frequency chart.
Figure 3. Grain size frequency chart.
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Figure 4. Radiocarbon dating sample location and depth.
Figure 4. Radiocarbon dating sample location and depth.
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Figure 5. Surface layer thickness contour map.
Figure 5. Surface layer thickness contour map.
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Table 1. Results of Radiocarbon Analysis.
Table 1. Results of Radiocarbon Analysis.
Sample Core #Description of SampleDepth of Sample (cm)Material/
Measured Radiocarbon
Age (ybp)
13C/12C RatioConventional Radiocarbon Age (*) (ybp)Calibrated Calendar Age
1160 ± 40−23.6‰1180 ± 40AD 770 ± 40
1940 ± 40−24.4‰1950 ± 40AD 0 ± 40
520 ± 40−24.9‰520 ± 40AD 1430 ± 40
640 ± 40+1.7‰1080 ± 40AD 870 ± 40
730 ± 40−25.1‰730 ± 40AD 1220 ± 40
1090 ± 40−0.6‰1490 ± 40AD 460 ± 40
310 ± 50−19.5‰400 ± 50AD 1550 ± 50
170 ± 50−23.2‰200 ± 50AD 1750 ± 50
1050 ± 40−24.4‰1060 ± 40AD 890 ± 40
Notes: * The conventional 14C age is the result after applying the 13C/12C correction to the measured age and is the most appropriate radiocarbon age. Quoted errors represent 2 standard deviations. DG-OS—Dark greenish-gray organic soil. DG-SSS—Dark greenish-gray sandy soil with shells. OS—organic sediment. AW—acid washes. AE—acid etch. CS—charred sediment. AAA—acid/alkali/acid.
Table 2. Radiocarbon Analysis, 1991.
Table 2. Radiocarbon Analysis, 1991.
Sample #Sample Depth (m)MaterialMeasured Radiocarbon Age (ybp)13C/12C RatioConventional Radiocarbon Age (ybp)
BH-3 a3.4–3.5Wood220 ± 60----
BH-3 b4.6Shell2890 ± 70+2.5‰3340 ± 70
BH-4 a1.7–1.8OS480 ± 60----
BH-4 b6.9–7.0OS4170 ± 100----
BH-4 c14.3–14.9Wood7400 ± 140----
BH-4 d15.2–15.3OS7100 ± 110----
BH-4 e22.9–23.0OSInsufficient carbon----
Notes: Quoted errors represent 1 standard deviation. OS—organic sediment.
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Laton, W.R.; Foster, J.H. Abrupt Late Holocene Closure of San Elijo Lagoon, Northern San Diego County, California. Coasts 2023, 3, 227-239.

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Laton WR, Foster JH. Abrupt Late Holocene Closure of San Elijo Lagoon, Northern San Diego County, California. Coasts. 2023; 3(3):227-239.

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Laton, William R., and John H. Foster. 2023. "Abrupt Late Holocene Closure of San Elijo Lagoon, Northern San Diego County, California" Coasts 3, no. 3: 227-239.

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