Peru’s penguins are on the brink. A super El Niño could make it worse.

The first time I was in Punta San Juan, the desert was flooded with birds. It was 2012, and I was making a short documentary film about the cormorants, pelicans and penguins that made this arid peninsula in southern Peru one of the largest gatherings of seabirds on Earth. At the time, this 133-acre reserve — a patch of rock and sand jutting into the frigid waters of the Pacific Ocean — was home to more than a quarter million seabirds, including 300,000 Guanay cormorants (Leucocarbo bougainvilliorum) and some 3,000 Humboldt penguins (Spheniscus humboldti).

One of the few species of desert penguin, the Humboldt live along the arid coast of Peru and Chile, where they nest in burrows dug into guano deposits or small cliff caves. Punta San Juan was home to the largest colony in Peru. By 2025, there were fewer than 500 penguins left.

Avian flu had spread through the reserve in 2022 and 2023, crashing seabird populations and spreading to marine mammals such as sea lions and seals. The climate pattern is characterized by months of warmer than usual sea surface temperatures in the eastern equatorial Pacific. Those warm waters pushed anchovy — the penguins’ main food source — deeper and farther out to sea.

Industrial fishing operations put even more pressure on the surviving animals. Ecologist Susana Cárdenas-Alayza, who has run the Punta San Juan Program in partnership with Cayetano Heredia University, the Peruvian government and American zoos for more than 20 years, is increasingly alarmed. As a scientist, Cárdenas-Alayza says, she is used to dealing with numbers and controlled variables, “but diseases and climate events escape my control.” Now, the reserve is facing a new threat: a potential “super” El Niño.

Soaring sea surface temperatures are disrupting the cold, fish-rich waters of the Humboldt Current, which flows past the peninsula. When I returned in July, much had changed from my first trip, when streams of penguins lined the cliffs of the reserve. This time I saw only five penguins — and several abandoned nests with cold eggs.

When food is scarce, penguins either stop reproducing or leave their nests altogether to search for a more favorable habitat, Cárdenas-Alayza says. They often starve along the way. The destruction has also been hard on the reserve’s volunteers, who protect the penguins in what Cárdenas-Alayza calls a “living laboratory.” For decades, volunteers from around Peru and the rest of the world have counted birds, recorded their diets and built artificial nests to keep penguin chicks safe.