Vehicles were originally allowed on the beach so that people could access the beach at low tide to dig for the world famous Pismo Clam. As long and the habitat was viable, the Pismo clam continued to flourish. The establishment of the ODSVRA has caused the traffic to increase to the degree that the habitat has been destroyed, and the Pismo Clam, still celebrated by the City of Pismo Beach, is no more.

The Western Snowy Plover, a small bird which builds its nest on open beach, is a Threatened Species. The Pismo Dunes Natural Preserve was established by the State Parks Commission through strict state and governmental laws designed to protect the environment, but the Western Snowy Plover, which nests in the Preserve, is threatened by noise, air pollution from motors, disrupted sand, fireworks, and possibly too, by children who love to chase birds, all of which come with the 2 million visitors a year who camp in the 1000 undesignated campsites of the ODSVRA located adjacent to the preserve. A study has shown that approximately 7% of Western Snowy Plover fledglings survive in the Nature Preserve.

The California Least Tern, an Endangered Species which is required by law to be fully protected, also nests in the Dunes, and is subject to the same assault by vehicles and campers as the Western Snowy Plover.

Vehicles routinely and in great numbers driving through the Arroyo Grande Creek disrupt and destroy the habitat of the Endangered Species Tidewater Goby, as well as the Steelhead Trout and the Red-Legged Frog.

Sea Lions sometimes come up onto the beach, but in at least one recent incident, a baby sea lion who ventured onto the beach found itself illegally ejected when it chose to shelter under a vehicle. The driver of the vehicle wanted to continue and the rangers removed the baby sea lion with a shovel and a broom. According to law, wild animals may not be molested in any way except by the appropriate wildlife specialist personnel.