"We've had to relocate tables inside because when people go out to the patio, some are like 'Oh my God. I can't handle the smell,'" said Christina Collignon, a hostess at Eddie V's, a steak and seafood restaurant perched on a cliff straight up from the guano-coated rocks.
On a recent afternoon, tourists on spring break walked along the sea wall. Some scrunched up their faces in disgust.
"It smells like something dead," said Meghan Brummett as she looked at the birds with her husband and children. The family was visiting from Brawley, a farming town two hours east of San Diego.
Biologists say the odor is the smell of success: Environmental protections put in place over the past few decades have brought back endangered species.
Cormorants and brown pelicans nearly became extinct in the 1970s because of the pesticide DDT. The brown pelican was taken off the federal endangered species list in 2010, and its population, including the Caribbean and Latin America, is estimated at more than 650,000. The total U.S. cormorant population is about 2 million.
La Jolla is a state-designated area of "special biological significance." That means California strictly regulates its waters to protect its abundant marine life, which also attracts birds.
"We're kind of a victim of our own success," said Robert Pitman, a marine biologist at the National Marine Fisheries Service in La Jolla. "We've provided a lot of bird protections so now we're getting a lot of birds. I think we're going to be seeing more of these conflicts come about, and I think we'll have to deal with them on a case-by-case basis. I think there'll have to be compromises all around."