How Does El Niño Affect South America?

El Niño reshapes weather across South America in a roughly predictable geographic pattern: it dries out the Amazon basin and northeastern Brazil while dumping heavy rain on the continent’s western coast and southeastern regions like southern Brazil, Uruguay, and northeastern Argentina. Those two opposing shifts, drought in the tropics and flooding along the Pacific coast and the southeast, ripple outward into fisheries, forests, glaciers, public health, and energy systems. The effects vary by region and by the strength of each event, but the footprint is continental in scale.

What El Niño Does to the Ocean and Atmosphere

El Niño begins with changes in the tropical Pacific. Westerly wind bursts near the dateline generate waves that travel eastward beneath the ocean surface toward South America, pushing the boundary between warm surface water and cold deep water (the thermocline) deeper than usual along the coast. That deeper thermocline means the cold, nutrient-rich water that normally wells up off Peru and Ecuador stays out of reach of surface mixing. Sea surface temperatures in the eastern Pacific rise, sometimes by several degrees above normal.¹

Those warmer waters heat the air above them and shift where tropical convection occurs. Moisture that would normally rise over the western Pacific and fall as rain over the Amazon instead gets redirected. Research has linked the transport of anomalous moist air during El Niño directly to drought in the Amazon basin and to increased precipitation over the southeastern United States.² In South America, the Walker circulation weakens, reducing uplift over northern regions and promoting sinking, drier air. Meanwhile, the subtropical jet stream strengthens across the continent’s southern tier, funneling more moisture into southeastern South America.³

Flooding on the Pacific Coast

The western coast of South America, particularly northern Peru and Ecuador, bears the brunt of El Niño’s rainfall. Warm water pooling along the coast triggers intense convection and downpours in areas that are normally semi-arid or even desert-like. During the austral summer of 2017, sea surface temperatures off northern Peru and Ecuador climbed roughly three to four degrees Celsius above normal, fueling intense coastal rainfall even though the broader tropical Pacific did not show a traditional basin-wide El Niño pattern.⁴

That 2017 event caused major flooding in Lima, Trujillo, and Piura, three of Peru’s largest cities. Mudflows ruptured water and sanitation networks, collapsing essential urban services.⁵ The physical damage extends beyond broken pipes. Semi-arid river catchments along the western Andes accumulate loose sediment during normal years because rivers lack the energy to move it. When El Niño rains arrive, river transport capacity surges. In the extreme events of 1982–83 and 1997–98, some semi-arid areas in Peru received rainfall roughly eight times higher than normal, and suspended sediment loads exploded from about four million tonnes per year during normal conditions to tens of millions of tonnes.⁶ That sediment chokes rivers, buries farmland, and worsens flood damage downstream.

Drought and Fire in the Amazon

While Peru’s coast drowns, the Amazon dries out. El Niño suppresses rainfall across much of northern and central Amazonia, and the effects go beyond parched forests. During the strong 2015–16 event, extreme drought struck the northern Brazilian Amazon. Roughly 59 percent of the study area in the state of Roraima experienced precipitation well below normal in January, and about 38 percent saw fire activity well above normal in at least one month between December 2015 and March 2016.⁷ Drought and fire together killed trees and released stored carbon in both undisturbed and human-modified forests.⁸

The carbon consequences are serious. Over the long term, South American tropical forests have acted as a net sink, pulling carbon dioxide out of the atmosphere. Across 123 monitored forest plots, that sink averaged about 0.38 tonnes of carbon per hectare per year before the 2015–16 El Niño. During and after the event, the sink effectively disappeared, dropping to a value indistinguishable from zero. Tree mortality spiked while growth barely changed, meaning the forests stopped absorbing carbon not because trees grew less but because more of them died.⁹ Modeling work supports the same conclusion: during eastern-Pacific El Niño years, the Amazon region flips from a carbon sink to a net carbon source.¹⁰ If droughts become more frequent, the Amazon could lose its role as a reliable carbon buffer, feeding back into the warming that drives more extreme events in the first place.¹¹

Wetter Conditions in Southeastern South America

El Niño’s drying effect in the tropics has a mirror image in the southeast. Southern Brazil, Uruguay, and northeastern Argentina tend to receive above-normal rainfall during El Niño years, with a signal that is more intense and more consistent than the opposite pattern seen during La Niña.¹² For agriculture, this is a mixed bag. Extra moisture can benefit crops like soybeans and rice during critical growing periods, but it can also cause flooding that damages harvests and infrastructure. The timing and magnitude of the rainfall anomaly vary from one El Niño to the next, so farmers in the Pampas and southern Brazil face uncertainty rather than a clean-cut blessing or curse.

Fisheries and the Humboldt Current

Few sectors feel El Niño as directly as Peru’s fishing industry. The Humboldt Current system, normally one of the most productive marine ecosystems on Earth, depends on cold, nutrient-laden water upwelling to the surface. El Niño suppresses that upwelling. Phytoplankton production drops, zooplankton volumes shrink, and the large copepods that anchovies depend on become scarce.¹³

The Peruvian anchoveta, which is one of the world’s most heavily harvested fish by volume, suffers on multiple fronts. Warmer water pushes temperatures well above the optimal range for egg hatching and larval survival. During the extreme events of 1982–83 and 1997–98, waters that are normally around 17°C during the critical larval development window soared above 23°C and even approached 25°C. By the time temperatures cooled enough, the plankton bloom that larvae need for first feeding had already passed. This timing mismatch between food availability and larval needs contributed to steep declines in landings.¹⁴ The economic fallout reverberates through coastal communities that depend on fishmeal and fish-oil exports.

Wildlife Beyond the Fisheries

The warm, nutrient-poor ocean conditions do not only affect commercially fished species. The Galápagos Islands, sitting astride the equator off Ecuador, provide a stark window into El Niño’s ecological toll. During the 1982–83 event, most seabirds in the archipelago stopped breeding. Blue-footed boobies abandoned all nesting attempts. Galápagos penguin populations fell by 77 percent, and flightless cormorant numbers dropped by 49 percent.¹⁵

Marine iguanas, which feed almost exclusively on intertidal algae, were hit just as hard. The 1982–83 event replaced most of the iguanas’ preferred algae species with a brown alga they could not digest, triggering widespread starvation. About 60 percent of the Santa Fe island population died between March and August 1983, with similar losses on other islands. Hatchlings from 1982 were nearly wiped out entirely.¹⁶ Later research during the 1998 El Niño confirmed that stress hormone levels in marine iguanas rose during the famine and varied between islands, with the hormonal response predicting which populations survived better than others.¹⁷ Populations do recover during the cooler, productive La Niña years that often follow, but strong back-to-back El Niño events could threaten long-term viability for species with slow reproductive rates.

Andean Glaciers and Water Supply

Higher up the continent, El Niño accelerates the retreat of tropical glaciers. These ice fields in Peru, Ecuador, and Bolivia supply water to millions of downstream users during the dry season, so their health is a practical concern, not just an environmental one. Mass balance measurements on Antizana glacier in Ecuador showed that the glacier lost mass year-round during El Niño periods but stayed close to equilibrium during La Niña. Higher air temperatures during El Niño favor rain over snowfall, reduce the reflective snow cover that shields ice from the sun, and weaken the winds that would otherwise convert some melting energy into sublimation.¹⁸

Peru’s Quelccaya Ice Cap, the largest tropical ice body in the world, showed even more dramatic losses during the 2015–16 El Niño. Net snow accumulation fell up to 64 percent below the mean for non-El Niño years, and the rate of ice wastage along Quelccaya’s margin was dramatically higher than during the previous fifteen years. The isotopic signature of the remaining snow confirmed that warmer, moisture-depleted conditions prevailed throughout the event.¹⁹ Each strong El Niño chips away at ice reserves that Andean cities and farms rely on for dry-season water, and those reserves are not being replenished fast enough between events.

Hydropower and Energy Systems

South America generates a large share of its electricity from hydropower, which means rainfall anomalies translate directly into energy supply risk. The countries most exposed are Colombia and Venezuela, where hydropower generation during drought El Niño phases can fall by up to half compared with neutral conditions. Argentina, Brazil, and Mexico also see reductions, though somewhat less severe.²⁰ Colombia has experienced electricity rationing during past strong El Niño events, and the risk of similar shortfalls grows as reservoir levels drop. Diversifying into wind and solar, which sometimes peak when hydropower dips, is one adaptation strategy that several Latin American countries are pursuing.

Public Health Consequences

El Niño’s climate shifts create conditions that favor disease. In Colombia, where malaria is endemic in lowland tropical areas, El Niño intensifies the normal annual cycle of both major malaria species. The outbreaks do not appear at unusual times of year but grow larger, amplified by warmer temperatures that speed mosquito development and altered rainfall patterns that change breeding habitat.²¹

Flooding and infrastructure collapse carry their own health risks. When mudflows rupture water and sanitation lines, as happened across Peruvian cities in 2017, waterborne diseases like leptospirosis and diarrheal illness surge.⁵ The 2015–16 El Niño was also linked to increased dengue and chikungunya incidence in other regions globally, though the mechanisms vary by location: in some areas rainfall anomalies concentrate breeding habitat for mosquitoes, while in others drought forces people and insects to share smaller water sources.²² Health systems across the continent have to prepare for a shifting mosaic of flood-related and drought-related threats during El Niño years, and the specific diseases depend heavily on what is already endemic locally.

Why the Future Looks More Intense

Climate models consistently project that extreme El Niño events will become more frequent as greenhouse gas concentrations rise. One analysis found that extreme events could roughly double in frequency under continued warming, driven by the eastern equatorial Pacific warming faster than the surrounding ocean.²³ Historical observations already show that both the frequency and intensity of strong El Niño events have been changing in line with background ocean temperature shifts, which reinforces the modeling projections.²⁴

One especially concerning finding is that the increased frequency of extreme events does not stop when warming stops. Even if global mean temperatures stabilize at 1.5°C above pre-industrial levels, deepening of the oceanic thermocline sustains faster warming in the eastern equatorial Pacific for up to a century afterward. That means future generations could face a higher risk of extreme El Niño events long after emissions peak.²⁵ For South America, where El Niño already triggers flooding, fishery collapses, drought-driven fires, glacier retreat, and disease outbreaks, more frequent extreme events would compound every one of those impacts.

Early Warning and Preparation

The good news is that El Niño is one of the more predictable climate phenomena, with useful forecasts often possible six to nine months ahead of an event’s peak. Seasonal forecasting has improved to the point where Latin American countries now have meaningful lead time to prepare. Public health systems can pre-position medical supplies, reinforce vector-control programs, and bolster water treatment infrastructure in vulnerable areas before the rains or drought arrive.²⁶

Efforts are also underway to push that warning window even earlier. Researchers have explored new indicators based on Pacific Ocean temperature indices that could signal the likely onset of an El Niño before official forecasts are issued, giving at-risk communities and humanitarian organizations additional time to consider protective actions.²⁷ The practical challenge is translating forecast information into action on the ground, especially in rural or underserved communities where institutional capacity is thin. Peru’s experience with the 2017 coastal event showed that even when the broader pattern is forecast, localized and unusual variants can still catch cities off guard.

Ancient Adaptations in the Andes

El Niño is not new to South America. The Moquegua Valley in southern Peru, despite receiving less than 50–100 millimeters of rain per year and sitting squarely in the path of ENSO-driven floods, supported rich and complex civilizations for millennia. Cultures including the Wari, Tiwanaku, and Chiribaya engineered sophisticated canal systems, hillside terracing, and extensive irrigation networks that allowed intensive agriculture even in hyper-arid conditions punctuated by periodic El Niño deluges. These ancient adaptations are a reminder that living with El Niño is a challenge South American communities have been navigating, and sometimes solving, for thousands of years. Modern infrastructure has yet to match the resilience some of those systems achieved.