Los Penasquitos Lagoon

This report on the Los Peñasquitos Lagoon was taken 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

Figure 1. Los Peñasquitos Marsh Natural Preserve

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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