The reserve is a dynamic ecosystem containing of five major plant communities.
Salt Marsh Community
Most of Bolsa Chica is salt marsh. The coastal salt marsh habitat is characterized by flooding of low-lying areas at high tide by salt water from the ocean. Plants in this community have adapted to a very special set of conditions. Salt water flows into the wetlands from both Anaheim Bay and an inlet near Seapoint Ave. Plants often have to deal with changing levels of water as a result of the tides. Primarily only halophytes (salt tolerant plants) can grow in this region. Coastal salt marshes are detritus-based ecosystems. This means dead plants and animals are at the base of the food pyramid, and that the decomposer community is of utmost importance in this ecosystem.
Coastal Strand/Sand Dune
Coastal sand dunes are dynamic and fragile habitats. Soils are sandy with little organic matter. Conditions are harsh with salt spray and stiff afternoon breezes that dry out plants. Winds can shift dunes with the seasons, moving them southward during winter storms and northward during summer storms.
Water percolates quickly through porous sand, but if plants put their roots down too deeply, they encounter seawater with high salinity. Life on dunes is rough for plants; they have adapted to harsh conditions by forming low-growing, spreading mats with shallow root systems. These plants can easily be uprooted by humans walking on them.
Most plants in this community have small hairs on their leaves that help them to collect moisture from the marine layer.
At Bolsa Chica, sand dune habitat is found along Pacific Coast Highway and in other parts of the reserve. Tern nesting islands are additional dune habitat.
Coastal Sage Scrub
Coastal sage scrub (CSS) is an assemblage of plants that are found on dry, south-facing slopes, usually near the coast up to an elevation of 3000 feet. CSS habitats are found between the coastal strand and chaparral zones, although many plants of the coastal sage scrub community can be found interspersed with chaparral.
Conditions in this habitat are cooler and drier than chaparral. However, fog along the coast provides enough moisture that keeps temperatures cool enough to prevent this region from being a desert.
Marshes in Southern California often dry up during the long dry season, or become quite restricted, so plants growing there must be tolerant of dry soils at least part of the year. Rushes, bulrushes (tulles), and sedges are common, and cattails are often found in the shallower water near the margins. Mule fat is found around the margins of more alkaline marshes.
Bolsa Chica has lost more freshwater wetlands than saltwater. Freeman Creek (a tributary of the Santa Ana River) and Wintersburg Creek once flowed into the wetlands year-round, with marshes that extended miles inland. Now freshwater at Bolsa Chica is restricted to four places:
- A brackish runoff pond at the end of Springdale Road
- A swale and cattail marsh fed by runoff from the Seacliff Golf Course
- A very small marsh about 5ft by 15ft at the south end of Bolsa Chica by PCH that is fed by runoff from PCH
- Brackish water upstream in Wintersburg Flood Control Channel
All of these freshwater wetlands are highly degraded and contain varying degrees of pollutants. Only the marsh fed by runoff from Seacliff Golf Course supports a significant stand of cattails and bulrushes.
There appears to be an additional source of freshwater that is very puzzling. Along the western boundary of the salt marsh in the inner bay bordering PCH, a narrow strip of cattails, bulrushes, and sedges separates the dunes from salt marsh in isolated spots. Some people have speculated there may be a series of freshwater springs running along the edge of the salt marsh at that location.
Riparian woodland habitat includes plants that grow along streams. These plants require more water than plants of the dry scrublands, and often have large leaves.
At lower elevations, the dominant trees are western sycamore, California bay laurel, mule fat, and willows (black, red, sandbar, and arroyo). At middle elevations white alder, big-leaf maple, and black or Fremont cottonwoods are added to the plant palette.
Riparian habitat is rapidly disappearing from Southern California due to stream channelization for flood control and development. As with all other habitats, when this habitat is destroyed, the birds and animals that rely on it are also lost.
At Bolsa Chica, there is a small strip of riparian woodland that grows in the runoff swale that carries water from Seacliff Golf Course down Huntington Mesa into Bolsa Chica.