The Santa Margartia River is normally sluggish and has many pools and marshy areas. The pH ranges from8.0 to 8.5. The vegetation of the Santa Margarita Ecological Reserve is largely comprised of coastal sage scrub and grassland. These plants are adapted to such environmental factors as summer drought, limited winter rains, shallow soils and fairly frequent fires. Some foreign species have begun to invade areas where fires have occurred.
Riparian vegetation exists along the river banks and in the washes.
Oaks occur sporadically in groves along the river. There are many introduced trees as well, such as Eucalyptus trees and fruit trees. Beavers are not native to the Santa Margarita River. The Santa Margarita river was not one of the three rivers into which beavers were introduced and the way in which beavers reached and colonized the Santa Margarita River is unclear. One possibility is that, during heavy winter storms, beavers living in other rivers may have been washed out to the ocean.