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. El Niño struck next. 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. In the summer of 2025, they even launched a “penguin patrol” to safeguard the Humboldts from workers harvesting guano, nitrogen-rich bird droppings essential for agriculture. Wanting to pitch in, the workers built a temporary, half-kilometer-long wall out of sacks of guano to shield the penguins on their daily walk to the sea.

Keeping research going — and morale high — in the emptying ecosystem has been one of the biggest challenges of Cárdenas-Alayza’s career. No one knows how long the current El Niño will last — or when the fish will return.

Nevertheless, Cárdenas-Alayza says she still has hope. Many species in Punta San Juan are philopatric, or loyal to their territory. That means that even when they leave in search of food or other resources, they eventually come back.

Biologist Patricia Majluf, who founded the Punta San Juan Program in 1979, shares one example of resilience: The El Niño event of 1997–98 decimated the reserve’s sea lions and seals. Penguin numbers dropped into the low hundreds. But the animals eventually mounted a remarkable recovery, helped by a major reduction in anchovy fishing quotas in 2006.

Scientists are busy preparing Punta San Juan for the animals’ return. Cárdenas-Alayza briefed incoming members of Peru’s Congress on the situation in July, and she and her fellow researchers are lobbying hard for stricter fishing quotas. They are also championing a new ecosystem restoration strategy, a collaborative framework that engages fishing communities, companies, students and even local chefs to help the reserve’s animals recover.

Back in Punta San Juan, Cárdenas-Alayza’s team is pressuring the government to reinforce a protective concrete wall around the reserve. In the meantime, they are trapping invasive species that prey on young birds, such as foxes and rats. They are also developing AI tools to speed data analysis from remote cameras monitoring breeding among the surviving Humboldt penguins.

As I prepared to leave, Cárdenas-Alayza, Majluf and I shared a meal of chifa, a Peruvian-Chinese cuisine that is a traditional Sunday dinner for Peruvian families. The three of us talked about our experiences teaching and people we had known at the reserve — and Cárdenas-Alayza teased Majluf, saying she was her “conservation mom.” It was at that moment that I realized what kept drawing me back to the reserve. I had come to document the region’s desert penguins, but I had learned so much more: Conservation isn’t just about science; it’s about relationships. At the end of the meal, we all opened our fortune cookies. Cárdenas-Alayza laughed when she saw hers: “Mountains are meant to be climbed.”