Plant Communities

 
Cordgrass (Spartina foliosa) forms robust stands along tidal channels in the northern reaches of the Reserve. Large stands of this species are rare in the other more disturbed southern California wetlands, and they are of particular importance as habitat for the endangered light-footed clapper rail (Jorgensen, 1975). Above the cordgrass-dominated community are found several succulents, including pickleweed (Sarcocornia pacifica) and saltwort (Batis maritima) as dominants, and annual pickleweed (Salicornia bigelovii) and sea blite (Suaeda esteroa). Alkali heath (Frankenia salina) is another dominant high-marsh plant. At higher elevations, these succulents grade into a dense matted cover of shoregrass (Monanthochloe littoralis). At the highest elevations, another species of pickleweed (Salicornia subterminalis) becomes co-dominant with shoregrass. 
The low-growing, open canopies of vascular plants in southern California marshes allow light penetration to the soil surface and subsequent development of lush algal mats (Zedler, 1982d). Filamentous bluegreen and green algae and dozens of species of diatoms form mats up to one centimeter thick on moist soils. These occur at all intertidal elevations. The early studies on the composition of these marsh algal mats were performed at Tijuana River Estuary in the 1970s. These algal mats are about as productive as the overstory salt marsh plants (Zedler, 1980) and actually play a more important role as a food source in the estuarine food chain (Williams, 1981; Zedler, 1982c). Reduced tidal circulation, natural flooding, prolonged excessive freshwater input, compaction by off-road vehicles, and the introduction of exotic species can cause changes in both salt marsh community structure and function (Zedler, 1982d). 
Salt marsh bird's beak (Cordylanthus maritimus) was once a common plant of the upper marsh but is now listed as endangered under the Federal Endangered Species Act. This plant likely owes its endangered status to the filling and destruction of upper marsh habitat in California. At the Tijuana River Estuary, salt marsh bird's beak occurs near areas with slightly disturbed soil surfaces, such as along the edges of paths and roads, sparsely vegetated openings, and depressions. 
 

Historical Context

 
In the past, an important source of disturbance to sensitive salt marsh vegetation has been the large number of undocumented immigrants from Mexico that enter the U.S. via the estuary. Until the mid-1990s, hundreds and occasionally thousands of individuals crossed the estuary every day, trampling the vegetation and creating numerous unnecessary trails. Although increased efforts by the U.S. Border Patrol have significantly diminished the foot traffic through the Reserve, the patrols have created a number of new roads, particularly in the southern portion. Some of these roads pass through some of the most sensitive habitat areas.
Areas disturbed by foot or vehicle traffic are slow to recover.