Lagoon view

Los Peñasquitos Marsh

Information taken from:
Natural Preserve and Lagoon

From Torrey Pines State Natural Reserve

Edited by Carl L. Hubbs, Thomas W. Whitaker, and Freda M. H. Reid
Published by The Torrey Pines Association

Physical Environment   Plants   Invertebrates   Fishes   Birds   Mammals   Conservation   Bibliography
 Map of the lagoon mouth at TPSR
Figure 1.  Los Peñasquitos Marsh Natural Preserve

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The Physical Environment

The lagoon marsh complex constitutes the northern part of the Reserve. The marsh is now carefully protected under its designation as a Natural Preserve. The area is closed to all boats and hiking except for the Flintkote Trail. The area was formed about 10 to 20 thousand years ago as a result of the melting of the polar ice caps at the end of the Fourth Glacial Period. As the sea rose, it flooded the valley cut by the young Los Peñasquitos River to form a deep embayment. Since that time, however, the sediment brought down by the river has filled in most of the valley, forming extensive mudflats so that now only relatively shallow channels and broad tidal pans .  During earlier periods, considerably more fresh water must have entered the lagoon than at the present time, because while describing Portola's trek from San Diego to Monterey in July 1769, Fr. Crespi spoke of the Soledad Valley (Sorrento Valley) as being "very green and grassy. " He also described a small village of Indians "with little straw houses" and a pool of water in an arroyo near the village.

Fresh water now enters the lagoon from several sources. Although most of the natural drainage flows through Los Peñasquitos Canyon, during periods of high rainfall some water enters the basin from Carmel Valley to the north and from Sorrento Valley to the south. The total watershed draining into Los Peñasquitos Lagoon is approximately 60,000 acres. In addition, water in the form of treated sewage effluent has been entering the southeast portion from two nearby sewage treatment plants. In 1970 plans were formalized for the discharge of the wastes through the Metropolitan Sewage System.

Evidence from the configuration of the major lagoon channels indicates the original ocean entrance to have been at the extreme southwest corner of the lagoon, where the south parking lot stands today. Later, however, the opening tended to meander northward so that when the first narrow gauge railroad was constructed in 1888 along the north side of the valley, railroad maps show the ocean entrance to be at the extreme northwest edge of the valley under the present northernmost highway bridge. The old McGonigle Road constructed in 1909 wound its way northward down the Torrey Pines Grade and along the sand dunes, crossing the lagoon near the present entrance.

Until 1925, man had not greatly interfered with the normal lagoon drainage. Then however, the building of the present Santa Fe Railroad caused the first damage. The new roadbed running through the center of the valley divided the lagoon into its present northeast and southwest portions, significantly altering the tidal current pattern. This alteration decreased the effective tidal flow to approximately one quarter of its pre-1925 values, so that by 1928, photographs showed the entrance channel to be choked with sand as far as the old McGonigle Road Bridge. When the coast highway was expanded in the 1930's, the low beach barrier was increased in height for the roadbed and the lagoon entrance was shifted southward one quarter mile to its present location near the old McGonigle Bridge. Most of the old bridge pilings have been removed to increase tidal flow but at low tide some of them may still be seen.

Apparently during earlier periods the combination of higher rainfall together with a larger lagoon area and a less restricted entrance provided sufficient flow to keep a channel open through to the beach. Such a continuous connection with the sea is important for the survival of a normal lagoon flora and fauna. Evidence supplied by the abundant remains of shellfish and other marine life found in nearby Indian kitchen middens indicates that the lagoon mouth was permanently open thousands of years ago. Under present conditions, however, a permanent opening cannot be naturally maintained and the marine life has diminished and at times has been almost eliminated. During exceptionally wet winters sufficient runoff may accumulate in the lagoon to break through the barrier bar naturally. If the bar is not breached in this manner the channel is often bulldozed open to alleviate the danger of flooding and to improve the health of the lagoon.

The recent history of Los Peñasquitos and most other Southern California lagoons has been one of short periods of connection with the sea, alternating with longer periods of stagnation. With the stopping of the normal tidal ebb and flow, evaporation during periods of negligible freshwater inflow may increase salinities to high values. One such period occurred in January, 1959, when a combination of high tides and storm waves carried sand high enough up the berm to block the channel. As a result, the salinity steadily increased over an eight month interval from a normal value of 34 parts per thousand to 639 parts per thousand. The salt content was so high that only a few hardy species of marine animals were able to survive. These were the California Killifish, the Bay Topsmelt and the California Mudsucker. Most of the other abundant fish and shellfish fauna that had flourished when the lagoon was open to the sea disappeared.

On the other hand, if the amount of fresh water added should exceed the amount lost by evaporation, the seawater may be excessively diluted causing distress to truly marine forms. The addition of sewage effluent (which began in 1962) lowered the surface salinity to approximately 13 parts per thousand by late 1966. Although low salt content in the surface water inhibited many species, the deeper waters retained a salinity approximately that of seawater, furnishing a tolerable habitat for a few marine forms. Although not optimal for strictly freshwater or marine organisms, this surface brackish water is ideal for the establishment of species such as Ruppia. In 1966 this plant covered the entire lagoon surface. However, when the high rainfall in early 1967 breached the bar, the inflow of tidal seawater restored salinities to near ocean values and it gradually disappeared. This introduction of fresh seawater with its many swimming and floating organisms quickly reestablished many elements of a normal estuarine biota.

Many species of plants and animals that characterize lagoon habitats and are found in nearby lagoons have not yet established themselves in Los Peñasquitos Lagoon. Noteworthy examples among the plants are the Cord Grass (Spartina foliosa) and the Eelgrass (Zostera marina), which normally dominate the mid-marsh and subtidal zones respectively of Mission and South San Diego bays. Among the animals, the California Homshell (Cerithidea californica) and the Smooth Chione (Chione fluctifraga), which are abundant in these same marsh zones in Mission and South San Diego bays, are conspicuously absent in Los Peñasquitos marsh.

Some of these plants and animals are known to have been present in Los Peñasquitos Lagoon in former times. For example, Chione is one of the most abundant shellfish in the nearby Indian kitchen middens and Cord Grass was recorded from the lagoon during a vegetation survey made in 1942.

Dissolved oxygen, needed for most biological activity, is generally high during the day in the surface waters but becomes very low at night. This reflects considerable photosynthesis during the daylight hours and excessive respiration and decomposition (which use up oxygen) in the dark. The low values found in bottom waters indicate high rates of organic decomposition and correspondingly high productivity rates. The plant nutrients (nitrate and phosphate) are high in the lagoon compared with coastal water, presumably because of the continuous input of sewage effluent. These nutrients stimulate copious plant growth, particularly when the lagoon is closed from the sea.

The lagoon environment is thus a highly variable habitat compared with the open ocean. It is not surprising that to survive in such an unstable environment, plants and animals must have considerably more tolerance than  evolved specialized structures and behavior patterns to survive these extreme conditions.

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Schematic drawing of marsh plants & animals
  Figure 2.   Salt Marsh plants

At first glance, the plant life of the Torrey Pines Lagoon appears to be unexciting. The salt marsh plants are almost all low growing and lacking in brightly colored flowers. These drab looking plants, however, merit far greater attention than they normally receive because they exhibit some beautiful examples of ecological adaptation. Existing midway between the marine environment of seaweeds and the land environment of the upland scrub, the salt marsh plants have evolved the ability to cope with both salt water submergence and long hours of exposure to sun and wind.

The key to the success of salt marsh plants is their ability to thrive in highly saline soil. Unlike their upland ancestors, which cannot survive if the salinity of the soil water rises above 5 %, the salt marsh plants may grow in soil salinities of up to 80%. Some species, such as Salt Grass and Glasswort, can survive even in environments where the soil surface is covered with a crust of salt crystals.

These salt marsh plants have adopted several different devices to enable them to overcome adverse salinity. Many species dilute the salt in their cells by storing large amounts of water; as a consequence, the plants are fleshy and resemble desert succulents rather than plants of an aquatic environment. Other salt marsh species rid themselves of salt by pumping it out through tiny glands that cover their leaves. A few of these plants store salt in their lower leaves, which are subsequently shed.

Figure 3.   Pickleweed, a characteristic plant of the lagoon.

Another important adaptation of salt marsh plants is their ability to tolerate the water-logged, clayey marsh soils that are frequently deficient in oxygen. Many of the salt marsh plants store air in large spaces in their roots and underground stems; some appear to have an internal ventilation system through which oxygen travels from the leaves to the smallest rootlets. The spreading underground network of salt marsh plant roots plays an important role in binding the muddy sediments of the marshland, thus preventing rapid erosion.      Approximately 30 species of salt marsh plants occur in Los Peñasquitos Lagoon. These species tend to be grouped into contoured zones or belts of vegetation that correspond with average tidal levels in the marsh (Figure 2). At the lowest tidal level in Los Peñasquitos salt marsh (closest to the lagoon channels), an abundance of Pickleweed (Figure 3) and patches of Alkali Heath are found. The Pickleweed (and related Salicornia,  Sarcocornia, and Anthrocnemum species) has succulent, jointed stems and tiny leaves that are reduced to membrane fringed triangles clasping the stem nodes. The flowers are minute and remain more or less embedded in the fleshy stems; only the yellow pollen sacs and the delicate white pollen receiving stigmas emerge from the stem, turning the flower bearing shoots into yellow or white fairy dusters in late summer. The Alkali Heath can be recognized by its dark green leaves, the edges of which are download. In late spring and summer, this plant becomes clothed in delicate rose pink flowers which are avidly sought by bees.

At higher elevations in the marsh (that area covered by salt water only during the high spring tides), several other plants appear among the Pickleweed and Alkali Heath. These high marsh plants include Salt Grass, Sea Lavender and California Seablite. The Salt Grass is characterized by slender, sickle shaped leaves that roll tightly inward during dry conditions. The Sea Lavender is most easily recognized in mid-summer when it sends up long shoots bearing filmy sprays of pale violet flowers in the center of a cluster of broad, leathery leaves. These leaves (and those of the Salt Grass and Alkali Heath) are frequently coated with a white film of salt that has been pumped out of the plant by an efficient method of biological desalination. In contrast to the Salt Grass and Sea Lavender, the short, densely packed leaves of the California Seablite are devoid of salt glands but are swollen with water that is used to dilute the  internally stored salt. The greenish flowers of the Seablite are small and inconspicuous; however, the leaves of this plant turn orange pink in late summer, forming a feathery splash of soft color.

The uppermost zone of the marsh is wetted only by extreme high spring tides and by storm waves. This zone is generally marked by the presence of Glasswort.  This plant is a succulent stemmed shrub, similar in appearance to  Pickleweed but brighter green, and with shorter, more slender stem segments.  On the southeast side of Los Peñasquitos Lagoon, where the upper lagoon channels give way to broad areas of bare salt pans, the Glasswort is often accompanied by two attractive spring annuals. One of these annuals, the Salt Marsh Daisy, forms conspicuous carpets of golden blossoms in early spring, following a good winter rain. Later in spring, Little Ice plant appears with sprays of tiny white flowers and leaves dotted by crystalline water storing glands;  as summer approaches, the flowers disappear but the color of the leaves ripens into an attractive orangeade hue.

On the southwest side of the Torrey Pines marshland, where the fresh  water of Los Peñasquitos Creek mingles with the saline lagoon water, the salt marsh vegetation gives way to a group of plants that are adapted to brackish water conditions. Most conspicuous of these plants are Cat-tails, large clumps of Spiny Rush that resemble over-grown porcupines, and low growing mats of Brass Buttons, which, as their name suggests, are dotted with small, golden, dislike flowers during much of the year.

The upland edge of the Torrey pines salt marsh, above the direct influence of tidal water, grades into typical coastal scrub vegetation. In this "transition zone" one will usually encounter familiar shrubs such as Lemonadeberry, Goldenbush, and Deerweed; these plants are also common in the main area of the Reserve.

On the southwestern side of the lagoon, near the highway, the upland  border takes the form of an old sand dune that probably formed the inland portion of the Torrey Pines beach prior to the construction of the highway.  (Figure 1)  This stabilized sand dune area is of interest because it represents a relict of the once extensive system of dunes that formerly lined the Southern California beaches. (Other relicts occur at the mouths of the Tijuana, San  Dieguito, and San Marcos rivers and in Camp Pendleton.)  At Los Peñasquitos,  the most conspicuous among the plants are the sand dune Evening Primrose, the  Coastal Cholla, and the Coastal Prickly Pear. These plants also occur on the   bluffs in the main Reserve area. Two species of plants grow on the sand dune that cannot be found elsewhere in the Reserve and are also very rare in Southern  California: the Beach Lotus, which is a spring annual with a spreading, mat like growth form bearing small 3 to 5 fingered leaves and clusters tiny orange and  red pea shaped flowers and the Golden Aster, a low growing perennial, which can be recognized by its silver haired leaves and daisy like, yellow flowers that  appear in early fall.
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Invertebrates of the Lagoon

Lagoon invertebrates
Figure 4.  Common invertebrate animals of the lagoon

Of the invertebrates occurring in the lagoon, the more  common and interesting ones are illustrated in Figure 4. The Bay Mussel,  which attains a length of 4 inches, is wedge shaped and blue black. It is found  attached by long fibrous threads to the pilings of the railroad bridge and to the rip rap near the northern beach parking lot. This is the "edible" mussel, prized  by seafood connoisseurs. However, potential consumers of the Bay Mussel and the related open coast California Mussel are warned not to eat them during the  summer months. At this time Public Health authorities proclaim that their flesh may be poisonous because the food of the mussel may include noxious  microscopic "red tide" planktonic organisms which occasionally flourish during  the warmer months.

The Common Littleneck Clam has many well developed radiating ribs and a few, less prominent, concentric ridges. The exterior is white to yellow  or tan with or without V-shaped brown markings. This clam may reach a size  of 3 inches and typically is found buried in black muddy sand.

The Jackknife Clam resembles a long and narrow whitish gray pocket  knife, in life partially covered by tough brown skin. This covering protects the  shell from dissolution from acid conditions in the sediments. It is rare to common and is used as fish bait locally. This clam was much more abundant  during earlier periods as indicated by the many empty shells in the sediments.

The Striped Shore Crab is dark green with numerous wavy stripes along  its back. This is the largest of the common lagoon crabs, reaching 3 inches in  width, and often may be seen scurrying about out of water, scavenging for  food.

The Mud flat Crab is smaller than the Shore Crab, and can be readily  distinguished from it by the yellowish buff color, and by the presence of many  hairs on the walking legs.

The Fiddler Crab is slightly smaller than the Mud flat Crab and is easily recognized from the others by its stalked eyes and by the one large claw brandished by the males. During courtship this claw is waved back and forth, thus suggesting the crab's name.
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Fishes of the Lagoon

At least 15 kinds of fish have been found in the shallow pools and channels of the lagoon. The more common species are described below.

The California Killifish is a small olive green fish with a flattened head. It grows to 5 inches in length and may be very abundant, particularly in shallow waters. It is highly salt tolerant, resisting the high salt concentrations when the lagoon is closed off from the sea.

The California Halibut is a flatfish, having eyes either on the left or right side of the head. The upper surface of this fish is greenish brown, sometimes mottled with small white spots. This is a commercially important food and sport fish, which, in offshore waters, may reach 5 feet in length and weigh 60 pounds. Breeding occurs in coastal waters and the juveniles make their way into bays and lagoons such as Los Peñasquitos, which they use as nursery grounds.

The Bay Topsmelt has a silvery lateral stripe and a transparent greenish dorsal surface. This common and hardy fish lives in schools and may grow to a length of 8 inches.

The Mudsucker has a long, slender, slimy dull olive body with a yellowish belly. It grows to 8 inches in length, and is common but usually difficult to find since it hides in the channel banks and hibernates in the bottom mud during the winter months. This extremely hardy fish will live for a week or more out of water if kept in damp seaweed. This characteristic makes the species valuable as live bait.

The Pipefishes, like the related seahorses, are biological curiosities in that the males have a brood pouch in which the females deposit eggs and the young undergo development. They occasionally reach 8 inches in length but are rare except in Ruppia beds, where, because of their coloring and shape, they may be indistinguishable from the blades of the plant.

The Southern Staghorn Sculpin has a large head with wide set eyes and an antler like spine in front of the gill openings. This common form may grow to a length of 6 inches. When disturbed, the spine is thrown upward and outward making a formidable defensive weapon.

The Arrow Goby is slender and small (less than 2 inches in length) and is very abundant, but because it is a sand mud color, it is almost impossible to distinguish unless it is moving.  This fish has the interesting habit of sharing the burrows of worms and ghost shrimps.
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Birds of the Lagoon

The majority of water birds which have been recorded from Los Peñasquitos Estuary are migratory waterfowl and shorebirds that rest and feed in the lagoon during their flight in fall and on their return in spring to their northern breeding grounds. The shorebirds  and waders frequently may be observed probing the mudflats for worms, clams and insects at low tide or resting in the salt pan areas at high tide. Diving birds, such as cormorants, grebes and pelicans, are most commonly seen in the deeper tidal channels near the lagoon entrance. The majority of ducks usually congregate in the large ponds on the southwest side of the lagoon where the  freshwater stream enters.

Relatively few birds are permanent residents of the lagoon area.  However, several showy species such as the stately Great Blue Heron, and the vociferous Black necked Stilt and Killdeer are often seen. The Stilts and  Killdeer nest on the dry salt pan area on the southwest side of the lagoon.

Several other birds are frequently seen in the lagoon area although they  ate not dependent on the marshland for their survival. The commonest bird in the Pickleweed vegetation is the dainty, speckle breasted Savannah Sparrow.  The flute like tones of the Western Meadowlark, and the guttural "kwaak" of the  Black crowned Night Heron are frequently heard at the western end of the marsh and the scarlet flash of the Red winged Blackbird is a common sight among the cat-tails and wild mustard at the eastern end of the lagoon. Two fairly common predatory birds are the slender, graceful Northern Harrier and the handsome Black shouldered Kite; both may be seen gliding over the salt marsh in search of small rodents and birds. The Kites, which only a few years ago were in danger of extinction, are becoming commoner in the Reserve, and  Red tail and Red shouldered Hawks, Pelicans and Ospreys are also occasional  visitors.

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Mammals of the Lagoon

Relatively little is known about the mammals that frequent the lagoon area since most of them are nocturnal and secretive in their movements. It is also doubtful whether any of the observed mammals are entirely dependent on the salt marsh for their existence. Most of them appear to live in the grassland, brush and dry bank areas adjacent to the marshland and to venture forth into the marsh to forage during periods of low tides.

Most conspicuous of these mammals are the Mule Deer that graze in the salt flats south of the lagoon. Rarely seen, but evident from tracks in this salt pan area, are the Coyote, Bobcat and Raccoon.  Abundant shells in the Raccoon scats indicate that they catch and eat the crayfish that abound in the salt flat area following winter rains.

A number of small mammals appear to forage for seeds, shoots, and insects in the grassy areas of the high marsh and in the adjacent Pickleweed. These include the Ornate Shrew, a minute velvet coated creature with a  voracious appetite and a vicious temper, the dainty Western Harvest Mouse, and  the dapper, white bellied Deer Mouse. The California Meadow Mouse, Pocket  Mouse and House Mouse may also occur in this area in large numbers.

Other common visitors in the upland areas of the marsh are the Audubon Cottontail and the Brush Rabbit. Ground Squirrel burrows and Pocket Gopher mounds along the railroad embankment suggest that these mammals may  also forage in the marsh.
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Conservation of the Lagoon and Marsh

The flora and fauna of Los Peñasquitos Lagoon and salt marsh obviously form a very different ecological unit from that of the upland portions of the Torrey Pines State Natural Reserve. At Present this flora and fauna is not as rare as that associated with the unique Torrey Pine trees; however, the fact that the coastal lagoans and marshlands of California are rapidly dwindling under the  impact of urbanization has prompted the State Division of Parks and Recreation to raise the status of Los Peñasquitos Lagoon from "State Park" (with free  public access and recreational use) to that of "State Reserve" (with restricted  access and usage) and now to "State Preserve" (the most restricted usage). This  label, which is pinned to only the rarest and most fragile of the state owned  lands, reflects the increasing concern of ecologists and wildlife managers for the progressive destruction of coastal wetlands, a habitat vital for the preservation of migratory waterfowl and certain species of fish and shellfish.

The "Preserve" Status of Los Peñasquitos Marsh and Lagoon will ensure the future protection of the lagoon flora and fauna from direct public misuse. Unfortunately, however, the natural boundaries of the lagoon ecosystem do not coincide with the fence lines of the State Preserve, but extend upstream to the watersheds of the creeks draining into the lagoon and the tops of the mesas surrounding the marshland. Here, far outside the Preserve boundaries, the removal of brush may result in erosion and the subsequent deposition of huge loads of silt in the lagoon channels; similarly, a city many miles inland may discharge sewage effluent into a creek that flows into the lagoon and thereby cause an accumulation of unnaturally high concentrations of plant nutrients in the lagoon waters.

The lagoon is thus vulnerable to far reaching man-made changes in addition to local environmental alterations.  Furthermore, the lagoon saltmarsh  complex is an extremely fragile ecosystem, the life of which depends on the maintenance of a regular ebb and flow of tidal water. Excessive silting of the channels will hasten the closure of the lagoon mouth and will accelerate the filling-in of the marshland.  Over enrichment of the lagoon waters will spark off unsightly algal blooms that lead to a syndrome of plant decay, oxygen depletion, fish kills, and unpleasant odors.

In March 1983, a Los Peñasquitos Lagoon Enhancement program began operation through cooperation of the California Coastal Commission and the Coastal Conservancy with assistance from the newly formed (and Conservancy approved) Los Peñasquitos Lagoon Foundation.  Members of the Foundation  board represent the State, City of San Diego, and San Diego County administration, as well as land developers and private environmental groups.  The collection of an impact fee from applicants for building permits within Los Peñasquitos watershed, as a mitigation measure, had resulted in the state policy for protection and restoration of the lagoon and wetlands. In March 1985, the  planned restoration was announced in the Los Peñasquitos Lagoon Enhancement  Plan, a guidebook approved for implementation of state restoration policy.

The planned program has proceeded so that tidal action approaches the stated goals, with more extensive work projected into the future.  Wetland acquisition has been achieved through state purchase of the 200+ acres of former San Diego Gas & Electric utility land which encompasses major lagoon channels into Torrey Pines State Natural Reserve.  Other additions to the south include approximately 20 acres of valuable wetland in Sorrento Valley. Stewardship has  been accepted for the 22 acre open space easement that extends from the Torrey  pines Extension to the lagoon below, south of Carmel Valley Road.

The Foundation continues in its main function which is to keep the lagoon mouth open, monitor physical changes, restore habitat, and improve channel circulation.

In a geological sense, all lagoons are ephemeral because the filling-in of the marshlands and channels eventually leads to their conversion to dry land.   The rate at which this filling process occurs, however, depends largely on the rate of silt deposition and accumulation of organic material in the lagoon. Los Peñasquitos Lagoon will not escape this ultimate fate, but a long remaining life span will depend on the foresight of the present generation of citizens who will determine whether this life span will be measured in thousands of years or merely a few decades.

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