San Diego County’s iconic coastal locations face triple threat from ‘Super El Niño’

San Onofre

At San Onofre State Beach, just south of the county line, sits a decommissioned nuclear power plant. Inside, 3.6 million pounds of highly radioactive spent nuclear fuel is being kept in long-term, underground storage. The plant was not constructed with long-term storage in mind.

With little room to act as a buffer, nuclear experts recently expressed concerns about long-term storage right on the beach. The facility is defended by a 30-foot sea wall, designed to withstand similarly sized tsunami waves. The spent fuel storage is surrounded by another 28-foot wall, according to Southern California Edison in 2022.

While the facility itself is protected, the surrounding San Onofre State Beach still faces erosion risks. A large cliff failure occurred during the 2015-2016 El Niño, and historic coastline scans by the Scripps Coastal Processes Group show consistent erosion along the coastal bluffs — slowly stripping away the sandstone supporting I-5.

Oceanside Harbor

Oceanside has spent decades managing the land around the harbor, the construction of which blocked sand from slowly shifting south — causing accumulation on the northern beach and persistent erosion on southern beaches, according to a U.S. Army Corps of Engineers study.

In contrast to other coastal areas, Oceanside’s northern beach widened as blocked sand accumulated during the 2015-2016 El Niño, according to Adam Young’s research.

The city of Oceanside reports that sand loss has caused 6.6 feet of retreat annually in some areas south of the harbor. After each winter, the Army Corps dredges sand from the mouth of the harbor onto retreating beaches and to support outlet pipes on the northern beach. CJW Construction, a contractor working with the Corps, dredged roughly 236,590 cubic yards after the 2015-2016 El Niño, as reported by Times of San Diego.

Local lagoons

San Diego’s lagoons face a similar risk from El Niño. Instead of sand getting washed away, powerful waves can pile sand onto inlets and estuaries, preventing the water behind from draining into the ocean. During the 2015-2016 El Niño, researchers found that more of these areas closed than normal. Inlets and estuaries close every year, but El Niño extended their closures — the water’s quality worsening while trapped.

“San Dieguito River, Santa Margarita River and Los Peñasquitos River all have lagoons that clog and can back up and flood surrounding areas,” Professor Chaddock explained. “They don’t have the same active channels that Carlsbad and others have.”

At Los Peñasquitos Lagoon, Adam Young’s research team found that inlet closure caused by the 2015-2016 El Niño caused damage to nearby roads and access ramps. The area saw substantial cliff erosion as well.

Prolonged closures prevent pollutants from being flushed out to sea. As these ocean outlets become blocked, oxygen levels in the stagnant water fall dangerously low, according to the National Oceanic and Atmospheric Administration. When fish aren’t getting enough oxygen to properly function, large-scale die-offs become increasingly likely — which occurred at the Los Peñasquitos Lagoon following a prolonged closure in 2013, according to the foundation dedicated to the area’s protection.

At San Dieguito Lagoon, inlet closures have caused dangerous drops in dissolved oxygen. An emergency excavation project followed a two month closure in 2006, when oxygen levels had fallen severely low and the area was unable to support aquatic life, according to the California Coastal Commission. Santa Margarita faces nutrient pollution that fuels algal growth and depletes oxygen, according to the San Diego Regional Water Quality Control Board.

The same El Niño event also prolonged closures at both lagoons further north. Santa Margarita remained closed for 44 days straight, according to a joint research project led by Scripps scientist Madeleine Harvey.

El Niño could raise local sea levels from 6 to 13 inches. With powerful Pacific storms already sending strong waves into Southern California, residents can expect prolonged closures in river outlet areas across San Diego’s coast.

North County’s coastal bluffs 

Coastal bluffs from Carlsbad to Del Mar provide the clearest examples of El Niño erosion and are at particular risk this year. During 2015-2016 storms, heavy rainfall destabilized the cliffs while powerful waves clawed away the base of the bluffs.

Cliff collapses can prove deadly, especially when beaches are in use. Suddenly, a massive 30-foot by 25-foot cliff collapse killed three women — a mother, daughter and aunt — at Grandview Surf Beach in Encinitas on August 2, 2019. The tragedy inspired a state bill to fund an enhanced coastal monitoring program and the development of an early landslide warning system in 2021, according to Scripps.

The danger extends beyond beachgoers. The same unstable coastal bluffs also threaten one of California’s most important transportation corridors. The 351-mile Los Angeles-San Diego-San Luis Obispo, or LOSSAN, rail corridor runs directly along the base of the bluffs. Landslides, erosion and bluff collapses have repeatedly threatened to cut off the track from reaching San Diego. 

In the short term, SANDAG and the North County Transit District are working together to stabilize the bluffs, installing 230 support columns and completing four stabilization projects since 2003. Phase five of the stabilization project began in 2024; construction of new support columns, extended seawalls and improved drainage will cost an estimated $88 million and is expected to be complete in 2027.

SANDAG acknowledges that these projects do not provide a permanent solution for ongoing erosion and sea level rise, warning that “large episodic bluff failures can result in more than 20 feet of bluff edge retreat in a single event.” The transportation agency is considering how tunnels and alternative routes could realign the rail corridor away from the coast.