How El Niño Affects Biodiversity and Ecosystems

Published: May 13, 2026 · 7 min read

A Planetary Perturbation

El Niño is not just a climate event — it is a biological event. The sudden reorganization of ocean temperatures, rainfall, and wind patterns that accompanies a strong El Niño reverberates through ecosystems on every continent and in every ocean. Species that have evolved within the bounds of normal climate variability can be pushed to their limits when El Niño amplifies or accelerates environmental stress. For some, the event is a temporary setback. For others, particularly when El Niño compounds with other human pressures, it can push populations toward local extinction.

The scale is staggering. A single strong El Niño can affect the breeding success of seabirds across the entire Pacific, trigger synchronized flowering and seed production in tropical forests spanning thousands of kilometers, and drive insect outbreaks that defoliate millions of hectares of temperate forest. Understanding these ecological impacts is essential for conservation planning in a warming world, where El Niño events are projected to become more extreme.

Marine Ecosystems: The First Domino

The most dramatic biodiversity impacts of El Niño occur in the ocean, and they start with the collapse of primary productivity. As upwelling weakens along the coasts of Peru, California, and West Africa, phytoplankton blooms diminish, and the entire marine food web suffers. In the eastern Pacific, the effects cascade upward through the food chain with remarkable speed.

Seabirds are among the most visible casualties. During the 1997–1998 El Niño, colonies of Galapagos penguins and flightless cormorants on the Galapagos Islands experienced near-total breeding failure. Populations of both species dropped by more than 50 percent. Blue-footed boobies, which rely on anchovies and sardines, abandoned nests across the Peruvian coast. Even albatrosses in the South Pacific — species that forage across vast ocean distances — struggled to find food for their chicks.

Marine mammals also suffer. South American sea lions and fur seals along the Peruvian coast lost pups to starvation as their prey base collapsed. In California, sea lion pups stranded on beaches in record numbers during the 2015–2016 El Niño, overwhelming wildlife rescue centers. The strandings were directly linked to the movement of their preferred prey — sardines and anchovies — into deeper, cooler waters that the sea lions could not reach.

Coral reefs, as discussed in detail elsewhere in this guide, suffer mass bleaching during El Niño. The 2016 event killed approximately 30 percent of the shallow-water corals on the Great Barrier Reef, transforming what had been a vibrant, three-dimensional habitat into a flattened, algae-covered plain. The loss of structural complexity reduced habitat for reef fish by roughly 50 percent in affected areas, with knock-on effects for the entire reef community.

Tropical Forests: Fire, Drought, and Fruiting

El Niño-induced drought transforms tropical forests in profound ways. In the Amazon, El Niño years bring reduced rainfall across the eastern and central basin, drying out the forest floor and creating conditions for wildfire — which is rare in undisturbed Amazonian forests that normally maintain high humidity year-round. During the 2015–2016 El Niño, thousands of fires burned across the Brazilian Amazon, releasing millions of tons of carbon and killing trees that had stood for centuries.

Borneo and Sumatra experience a similar pattern. The 1997–1998 El Niño coincided with one of the worst fire seasons in Southeast Asian history, as drought-parched peat forests burned for months under a thick haze that blanketed the region. Orangutan populations, already critically endangered, suffered direct mortality from fire and smoke, as well as habitat loss that persisted for years after the flames were extinguished.

Paradoxically, El Niño also triggers one of the most spectacular biological events in the tropics: mass flowering and fruiting in Southeast Asian dipterocarp forests. These trees have evolved to flower synchronously after a drought cue, and El Niño years often produce "mast" events in which the entire forest fruits simultaneously. This overwhelms seed predators, ensuring that at least some seeds survive. However, the same mast events also trigger population explosions of wild boar and other seed-eaters, followed by crashes when the fruit is gone.

Terrestrial Vertebrates: Winners and Losers

El Niño produces winners as well as losers. In the Galapagos, finch populations — the very birds that inspired Darwin's theory of natural selection — fluctuate dramatically with ENSO. During El Niño, increased rainfall on the islands triggers a burst of plant growth and seed production, and finch populations soar. The 1982–1983 El Niño produced a finch population explosion that allowed scientists to document natural selection in action: birds with beak sizes suited to the abundant small seeds survived better than those specialized for larger, harder seeds.

In the Atacama Desert, one of the driest places on Earth, El Niño transforms the landscape. Rainfall that may not have fallen in decades triggers a "desierto florido" — a flowering desert — in which dormant seeds germinate en masse, carpeting the ground in color. Insect populations explode, followed by lizards, birds, and rodents. The bloom is brief, but it sustains populations that would otherwise dwindle to near-invisibility.

For many species, however, El Niño is unambiguously harmful. In Australia, the extreme heat and drought associated with the 2019–2020 positive IOD (reinforced by a weak El Niño) contributed to the catastrophic bushfires that killed an estimated 3 billion animals. In southern Africa, El Niño droughts concentrate remaining water sources, increasing competition and predation risk for species like elephants, buffalo, and antelope.

Ecosystem Resilience and Recovery

The capacity of ecosystems to recover from El Niño depends on the severity of the event, the frequency of recurrence, and the presence of other stressors. A forest that burns during an El Niño but then receives normal rainfall in subsequent years can regenerate, especially if it was not burned again. But intervals between severe El Niño events are shrinking. Global warming means that what used to be a "once in a century" event in 1982 has become a "once in a decade" or more frequent occurrence.

Marine ecosystems face the same pressure. Upwelling ecosystems can rebuild their fish populations within a few years of a strong El Niño, but only if fishing pressure is reduced during the recovery period. When overfishing is combined with the natural collapse caused by El Niño, the recovery can take much longer — and in some cases, the ecosystem tips into a different state, dominated by different species that may be less productive and less valuable.

Conservation in the ENSO Era

Conservation planning must account for ENSO. Protected areas designed without considering climate variability may fail to protect species during El Niño years, when animals move in search of food and water. Dynamic management strategies that adjust fishing quotas, fire management protocols, and wildlife protection efforts based on ENSO forecasts represent the cutting edge of applied conservation science. The El Niño that is being forecast today is the same event that will determine the breeding success, movement patterns, and survival of countless species in the months ahead — and our ability to anticipate it is a powerful conservation tool.

Explore more at the El Niño Guide — comprehensive climate science explained.