El Niño weakens or shuts down the normal upwelling of cold, nutrient-rich water from the deep ocean, with consequences that ripple through marine food webs from microscopic plankton to fur seals and commercial fisheries. The mechanism centers on the relaxation of the trade winds that ordinarily push surface water aside and allow deep water to rise. When those winds falter during El Niño, the thermocline sinks, the nutrient pipeline stalls, and some of the most biologically productive waters on Earth become comparatively barren. The story, though, plays out differently depending on where you look and what flavor of El Niño shows up.
What Drives Upwelling in Normal Years
In the tropical Pacific under ordinary conditions, steady trade winds blow from east to west along the equator. That wind stress drags surface water westward and, through the Coriolis effect, deflects it away from the equator. Deep, cold water rises to replace what moves away. East of the international date line, this divergence is especially strong, and the nutrient-rich waters carried upward by the Equatorial Undercurrent fuel some of the highest biological productivity found anywhere at low latitudes.1PubMed Central. Ocean dynamics, not dust, have controlled equatorial Pacific productivity over the past 500,000 years Along coastlines in places like Peru, Oregon, and California, a related process occurs: winds blowing parallel to the shore push surface water offshore, and cold water wells up from below to take its place. These coastal upwelling zones are narrow strips of ocean that punch far above their weight in productivity and fishery output.
How El Niño Disrupts the System
An El Niño event begins when the trade winds weaken across the central and western Pacific. Warm surface water that had been piled up in the western Pacific sloshes eastward, and downwelling Kelvin waves propagate across the basin along the equator. During the 2002–2003 event, for instance, energetic downwelling Kelvin waves forced in the western-central Pacific were tracked crossing the entire equatorial Pacific.2Journal of Geophysical Research: Oceans. The 2002/2003 El Niño: Equatorial waves sequence and their impact on sea surface temperature These waves depress the thermocline in the eastern Pacific, pushing the boundary between warm surface water and cold deep water much deeper than usual. Since the thermocline roughly tracks the nutricline, the layer where dissolved nutrients are concentrated also drops out of reach of the normal upwelling circulation.
The result is a double hit. First, the weakened winds reduce the physical force driving water upward. Second, even where some upwelling persists, the water being pulled to the surface is now drawn from above the deepened nutricline and carries far fewer nutrients than normal. It is this combination that makes El Niño so damaging to marine productivity.
The Peruvian Coast Takes the Hardest Hit
Nowhere is the effect of El Niño on upwelling more dramatic than along the coast of Peru, within the Humboldt Current system. Normally one of the richest fisheries on the planet, this region depends on a steady supply of cold, nutrient-laden water reaching the surface. During El Niño, coastal-trapped waves propagating poleward from the equator deepen both the thermocline and the nutricline along the Peruvian shelf. Research on the Peruvian upwelling system found that while the winds actually become more favorable for upwelling during El Niño, a compensating shoreward geostrophic current near the surface offsets that wind-driven lift. The depth from which upwelling draws water stays about the same, but the nutrient content of that water drops sharply, and a deeper mixed layer further hampers phytoplankton growth.3Journal of Geophysical Research: Oceans. Impacts of El Niño events on the Peruvian upwelling system productivity
There is a counterintuitive wrinkle here. Even though the Equatorial Undercurrent weakens during El Niño, the flattening of the equatorial thermocline actually brings the undercurrent’s waters closer to the Peruvian coast. Studies tracing the origin of upwelled water found that during warm events, a greater proportion of Peru’s upwelling can be traced back to the Equatorial Undercurrent, while during La Niña, the source is more local.4Ocean Science. Interannual Variability in contributions of the Equatorial Undercurrent (EUC) to Peruvian Upwelling The shift in source water matters because it changes the chemistry of what arrives at the coast, and during El Niño, what arrives is nutrient-poor.
Phytoplankton Collapse and the Productive Zone
The biological response is swift and visible from space. During the 2017 Coastal El Niño off northern Peru, wind reversals favored downwelling, choking off the upward transport of nutrients. Chlorophyll-a concentrations showed strong negative anomalies, dropping by more than 3 milligrams per cubic meter. The High Productive Zone, a band of phytoplankton-rich water that normally extends roughly 300 kilometers offshore, contracted to about 25 kilometers from the coast over just two months. Its total area shrank by up to 130,000 square kilometers in March 2017 alone.5Progress in Oceanography. Chlorophyll response and High Productivity Zone contraction in northern Perú during the 2017 Coastal El Niño That is an area larger than many countries, essentially switching from highly productive to near-barren in weeks.
Off the California coast during the onset of the 1997–1998 El Niño, a similar nutrient drawdown was documented. As surface waters warmed, concentrations of nitrate and silicic acid fell steadily. Diatoms, the large phytoplankton that usually dominate productive upwelling zones, contributed less to total biomass, though the remaining community still managed to maintain moderate rates of new production.6Journal of Marine Systems. Siliceous plankton dominate primary and new productivity during the onset of El Niño conditions in the Santa Barbara Basin, California The ecosystem does not shut down entirely; it shifts toward smaller, less nutritious phytoplankton species, which is bad news for the animals further up the food chain that depend on the large, energy-rich diatoms.
Effects on the California Current
The California Current System stretches from British Columbia to Baja California and is the eastern Pacific’s other major coastal upwelling region. El Niño’s influence here arrives through two pathways. Coastally trapped waves from the tropics propagate poleward and depress the thermocline along the coast. At the same time, shifts in atmospheric pressure patterns can alter local wind forcing. The general picture is that El Niño produces weaker-than-normal upwelling and source waters that are unusually shallow, warm, and fresh. The peak disruption in vertical transport occurs about a month after El Niño peaks in midwinter, before the spring upwelling season begins. But the change in source-water density persists longer, carrying over into spring and summer, when upwelling is normally at its most productive.7Journal of Geophysical Research: Oceans. ENSO and the California Current coastal upwelling response Because nitrate concentration tracks density in this region, El Niño may actually have a bigger effect on the nutrient content of upwelled water than on the volume of water being upwelled.
The timing dimension matters for ecosystems. El Niño years are characterized by delayed and weak upwelling in the central California Current.8Geophysical Research Letters. Phenology of coastal upwelling in the California Current That delay means the spring bloom, which normally synchronizes with the breeding and feeding schedules of everything from krill to seabirds, starts late and starts weak. The 2015–2016 El Niño provided a striking case study: remote forcing through coastally trapped waves drove early warming anomalies, but an unusual onset of upwelling-favorable winds in autumn 2015 temporarily offset the warming in the central part of the system. Even so, low-nutrient anomalies persisted, and phytoplankton abundance remained anomalously low through the 2016 upwelling season.9Geophysical Research Letters. Local atmospheric forcing driving an unexpected California Current System response during the 2015–2016 El Niño The upwelling came back, in other words, but it brought impoverished water.
Nutrient Chemistry Changes
El Niño does not just reduce the quantity of nutrients reaching the surface; it changes the ratios. Off Oregon during El Niño conditions, reduced upwelling caused severe nitrogen limitation during what should have been the productive upwelling season. At the same time, enhanced poleward flow of warm, salty subtropical water introduced source waters with anomalously low ratios of nitrogen to phosphorus.10Progress in Oceanography. El Niño related variations in nutrient and chlorophyll distributions off Oregon Nitrogen is typically the nutrient that limits phytoplankton growth in these systems, so skewing the ratio makes the limitation even worse. The community of organisms that thrives depends heavily on which nutrients are available and in what proportions, so these chemical shifts can reshuffle the species mix even beyond what warming alone would cause.
The Food Web Unravels Upward
When the base of the food web shrinks, the effects cascade. Anchoveta, the small schooling fish that dominates Peruvian fisheries, depends on the synchrony between plankton blooms and the timing of larval fish development. Analysis of the severe El Niño events of 1982–1983 and 1997–1998 showed that abnormal warming disrupted this synchrony, creating a mismatch between plankton availability and early-stage fish larvae that likely reduced larval survival and, eventually, fishing yields.11ICES Journal of Marine Science. Phenological mismatch contributes to anchoveta landings collapse under El Niño and climate change in the Peruvian upwelling system
At the top of the food web, the consequences are grim. During the 1982–1983 El Niño, marine mammals in the Galápagos and along the Peruvian coast were severely affected by the acute food shortage. The Galápagos fur seal population lost nearly all individuals in its four youngest age classes, along with roughly 30 percent of adults. All larger territorial males disappeared and presumably starved. The Galápagos sea lion population lost most of its 1982 cohort and had a greatly reduced birth rate the following season. South American fur seals and sea lions on the Peruvian coast suffered high mortality as well.12Oceanography Series. El Niño’s Effect on South American Pinniped Species These are not minor fluctuations. The loss of multiple year classes in a long-lived mammal takes decades to recover from.
A Surprise on the Seafloor
Not every effect of El Niño on upwelling zones is negative. Off the coast of central Peru, the normal upwelling system produces high productivity at the surface but creates a vast oxygen minimum zone at depth. The seafloor beneath this zone is largely lifeless under normal conditions, too oxygen-starved to support most animals. When El Niño suppresses upwelling and reduces surface productivity, less organic matter sinks and decomposes, and the oxygen minimum zone relaxes. During both the 1982–1983 and 1991–1993 El Niño events, researchers documented dramatic recolonization of the normally hypoxic seafloor. Species counts surged from near zero to as many as 24 species. During the stronger 1982–1983 event, peak faunal density was five times higher and mean biomass twice as high as during the weaker 1991–1993 event, but even the weaker event caused a broad-scale shift in species composition and trophic structure on the bottom.13Marine Ecology. Impact of Two “El Niño” Events of Different Intensity on the Hypoxic Soft Bottom Macrobenthos off the Central Peruvian Coast So while the surface ecosystem suffers, the deep benthos gets a reprieve.
Not All El Niño Events Are Created Equal
Oceanographers increasingly recognize that El Niño comes in at least two distinct flavors. The classic, or Eastern Pacific, variety features maximum warming concentrated in the far eastern equatorial Pacific. The Central Pacific variety, sometimes called El Niño Modoki, centers its warming anomaly near the date line. The upwelling response differs between the two. Analysis of the connection between these event types and coastal upwelling intensity found that Central Pacific events tend to reduce upwelling intensity, whereas Eastern Pacific El Niño events can actually be followed by increased upwelling, with regional differences depending on the coast in question.14Journal of Marine Science and Engineering. El Niño–Southern Oscillation Diversity: Effect on Upwelling Center Intensity and Its Biological Response This distinction matters for forecasting. Knowing that an El Niño is developing is not enough; you need to know where the warming is centered to predict what will happen to a given upwelling system.
The La Niña Mirror Image
La Niña does roughly the opposite. Trade winds strengthen, the thermocline shoals in the east, and upwelling intensifies. The conventional expectation is that phytoplankton biomass in the tropical Pacific should be roughly proportional to La Niña intensity because of enhanced nutrient supply from stronger equatorial upwelling.15Limnology and Oceanography Letters. Amplifying effects of multiyear La Niña on phytoplankton biomass in the tropical Pacific Recent work suggests that multiyear La Niña events can amplify phytoplankton biomass beyond what a single-year event of similar intensity produces, a cumulative effect that does not have an obvious parallel during El Niño. The asymmetry between the two phases of ENSO means that the long-term average productivity of these upwelling zones is shaped not just by how often El Niño and La Niña occur but by how long each phase lasts.
El Niño’s Reach Beyond the Pacific
The Pacific is the epicenter, but El Niño’s fingerprint shows up in upwelling systems on the other side of the world. In the Benguela Current off southern Africa, the leading mode of upwelling variability during austral summer and fall correlates strongly with sea surface temperature and sea-level pressure in the equatorial Pacific, in a pattern that resembles ENSO during its peak season. Winter upwelling winds off North America’s west coast also respond to atmospheric teleconnections with the equatorial Pacific, and strong episodic wind events driven by those teleconnections can disrupt ecological systems.16Journal of Marine Systems. A comparison of modes of upwelling-favorable wind variability in the Benguela and California current ecosystems The connection is not always straightforward: local weather can amplify or counteract the remote signal, as the 2015–2016 event demonstrated off California.
When El Niño and the Pacific Decadal Oscillation Overlap
El Niño does not operate in isolation. The Pacific Decadal Oscillation, a slower climate pattern that shifts on timescales of decades, modulates how strongly ENSO affects upwelling and productivity. When the PDO is in its positive phase and an El Niño arrives, the two reinforce each other: sea surface temperatures rise more, wind speeds drop further, and vertical mixing weakens, starving the surface of nutrients. In the Yellow Sea, for instance, spring phytoplankton bloom intensity during years combining a positive PDO with El Niño was about 53 percent lower than during years combining a negative PDO with La Niña.17Ocean-Land-Atmosphere Research. In-Phase Pacific Decadal Oscillation and El Niño–Southern Oscillation Enhance the Interannual Variability of Spring Blooms in the Yellow Sea The phase of the PDO also appears to modulate the period and expression of ENSO itself in the sedimentary record, as seen in northeast Pacific productivity proxies spanning centuries.18Quaternary International. Influence of the Pacific Decadal Oscillation, El Niño-Southern Oscillation and solar forcing on climate and primary productivity changes in the northeast Pacific For anyone trying to anticipate how the next El Niño will affect a specific upwelling region, the background state of the PDO is a critical piece of the puzzle.
What Climate Change May Do to the Relationship
A major open question is how warming oceans will alter El Niño’s effect on upwelling in the coming decades. A review of climate change impacts on the world’s four major eastern boundary upwelling systems found some consistent trends: upwelling is intensifying at higher latitudes, near-coastal temperatures are warming less where upwelling strengthens, and water-column stratification is increasing with a shallowing mixed layer.19PubMed. Climate Change Impacts on Eastern Boundary Upwelling Systems But the review also highlighted significant uncertainty about how the sometimes-competing changes in upwelling intensity, source-water chemistry, and stratification will ultimately affect productivity and ecosystem structure. Stronger upwelling winds do not guarantee more productive waters if the water being pulled up is warmer and more nutrient-depleted to begin with. And if climate change shifts the frequency or character of El Niño events, the intermittent disruptions to upwelling zones could become harder to predict and more difficult for ecosystems to recover from between events.
Tracking the Signal in Real Time
Forecasting how El Niño will affect a specific coast depends on detecting the event early and understanding its spatial structure. The global network of Argo floats, autonomous instruments that profile the ocean’s temperature and salinity from the surface to about 2,000 meters, has transformed this capability. Machine learning applied to Argo temperature profiles can identify the vertical restructuring of the water column that accompanies El Niño, such as the tilting of the thermocline, by detecting when profiles shift from one statistical cluster to another.20Journal of Geophysical Research: Oceans. El Niño Detection Via Unsupervised Clustering of Argo Temperature Profiles Approaches like these complement traditional monitoring by capturing the subsurface changes that determine whether upwelling will bring nutrient-rich water or nutrient-poor water to the surface in the months ahead. For fisheries managers in Peru, ecosystem forecasters in California, and conservation biologists in the Galápagos, the difference between getting that prediction right and getting it wrong can be measured in collapsed fisheries, starving wildlife, and billions of dollars.