Today, Bonita Creek is a thriving riparian woodland with wetlands, and coastal sage scrub community that serve as natural habitats for wildlife. It still serves as a flood control channel; it provides biological filtration of the runoff from the surrounding watershed; and it continues to provide a wildlife movement corridor linking the San Joaquin Hills and the Upper Newport Bay.

Bonita Creek is a popular bird-watching site where more than 70 species of birds have been seen, including endangered species such as least Bell’s vireo. California gnatcatchers - a threatened species - live in the coastal sage scrub. Invertebrates, small mammals, and larger mammals such as coyote, bobcat, and mountain lions also use the habitats within Bonita Creek.