With the loss of a majority of California's wetlands to rapid urban development, the Salton Sea has become critical to the survival of millions of migrating birds as a stopover along the Pacific Flyway. The refuge provides habitat for some 2.5 million wintering geese, ducks, and grebes, including support for 90% of the North American population of the eared grebe, 80% of the white pelicans, 45% of the endangered Yuma clapper rail, along with significant populations of brown pelicans, bald eagles, peregrine falcons, and even tropical marine birds in summer.

In 1996, a devastating outbreak of avian botulism killed 14,000 pelicans, including the endangered California brown pelican, as well as 19,000 birds of other species. Throughout the summer, volunteers fought to save as many birds as they could, and prevent the disease from spreading to other species. In 1998, the refuge also suffered a huge outbreak of Newcastle's disease among crested cormorants and avian cholera among ducks and geese, which killed 17,000 birds.

The refuge now runs daily airboat patrols around the Sea looking for sick birds. Early detection is especially helpful in preventing avian botulism, as individual pelicans can be saved, as well as preventing the spread of the disease. In 1997, the citizens of Imperial Valley donated $92,000 towards the building of a wildlife hospital. This, along with the creation of other infrastructure, has allowed the refuge to better control avian botulism and other diseases.

The refuge offers visitors fantastic bird watching, waterfowl hunting, hiking trails, and a visitor center complete with a glass case full of taxidermied birds. The refuge has several full-time staff, scientists, a fleet of airboats, a bird hospital, and a crematorium for the disposal of dead birds.

It is also a confirmed rumor that around a dozen flamingos mysteriously call the refuge home. Some explanations for this local peculiarity include a 1950's escape from the San Diego Zoo or a house fire of an exotic bird dealer.

The park was dedicated to Salton Sea advocate Sonny Bono in 1998, after his death in a tragic skiing accident. After years of service, Superintendent Clark Bloom retired in 2002 in order to move back to his native Arizona.

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