Efforts at protection of the least Bell's vireo and the Willow Flycatcher have concentrated on these two major causal factors. Cowbird trapping has been conducted extensively in some portions of the Santa Ana watershed, with most of the focus of SAWA's efforts on the Prado Basin and the Hidden Valley Wildlife Refuge. A large scale population study has also been conducted in this area in conjunction with the Orange County Water District and the U.S. Fish and Wildlife Service. In addition, vireo surveys have begun in San Timoteo Creek, with cowbird trapping to begin shortly. SAWA's efforts of arundo and saltcedar eradication within the basin are also anticipated to benefit vireos (regrowth of native vegetation will provide vireo habitat). While the vireo continues to be an endangered species, there is some indication that they are recovering in the Santa Ana Watershed. The number of nesting pairs of vireos has steadily increased since 1986.

The Riverside-Corona Resource Conservation District has constructed a native fish stream to help augment native fish populations in the Santa Ana River Watershed and its associated tributaries. The three fish that are currently in the stream are the Santa Ana Sucker (Catostomus santaanae), Arroyo Chub (Gila orcutti) and the Speckled Dace (Rhynichthys osculus ssp). All of these fish were once common on the river and its tributaries, but over time, sedimentation, runoff, water diversions and flood control have all combined to change the hydraulics of the river. The Santa Ana Sucker was once in abundance in the drainage, and is in small numbers in the upper San Gabriel River and the Santa Clara, but because of the marked decline in numbers of these fish, the U.S. Fish and Wildlife Service recently listed the sucker as threatened under the Endangered Species Act.