El Niño disrupts fishing across much of the world by warming surface waters, suppressing the nutrient supply that feeds marine food chains, and pushing commercially important fish species into unfamiliar territory. The effects are not uniform: some fisheries crash while others see temporary windfalls, and the severity depends on whether an event is moderate or strong. What makes El Niño so consequential for fishing is that it reaches into nearly every link of the chain, from microscopic plankton to billion-dollar global commodity markets.
How Warming Waters Starve the Food Chain
Under normal conditions, cold, nutrient-rich water wells up along the western coasts of the Americas, especially off Peru and Ecuador. That upwelling feeds explosions of phytoplankton, which in turn support the small fish, squid, and larger predators that fishing fleets depend on. During El Niño, this conveyor belt weakens. The thermocline and nutricline, the layers where temperature and nutrients change sharply with depth, sink deeper. Even though winds that normally drive upwelling can actually intensify, a compensating shoreward current near the surface keeps nutrient-poor warm water in place along the coast. The water being pulled up still comes from the same depth, but it arrives with far fewer nutrients, and the deeper mixed layer makes it harder for phytoplankton to grow.
1Journal of Geophysical Research: Oceans. Impacts of El Niño events on the Peruvian upwelling system productivityObservations during the 2015–16 El Niño confirmed this pattern across a broad swath of the eastern tropical Pacific: nutrient concentrations dropped through the upper 200 meters of the water column, while oxygen levels rose in the mid-water zone where nutrients would normally be concentrated.
2Ocean Science. Observed El Niño conditions in the eastern tropical Pacific in October 2015Less nutrients means less phytoplankton, and that reduction ripples upward through the food web. Satellite analyses show that during El Niño events, tropical ocean chlorophyll, a proxy for phytoplankton abundance, drops by roughly 7 to 9 percent across the tropics. Small increases occur at higher latitudes, but nowhere near enough to offset the tropical losses.
3Frontiers in Marine Science. Impact of El Niño Variability on Oceanic PhytoplanktonThe composition of what does grow also shifts. Even when total phytoplankton abundance stays roughly the same in some coastal areas, the community tends to be dominated by smaller cells during El Niño. Smaller cells support less productive food webs, meaning less energy is available for the fish that fishers want to catch. Water transparency climbs during these periods, a visible sign that the biological engine driving the ocean’s productivity has throttled down.
4Ecological Indicators. Changes in phytoplankton vertical distribution during an El Niño eventThe Peruvian Anchoveta Collapse
No fishery on Earth illustrates El Niño’s destructive potential as starkly as the Peruvian anchoveta. In a normal year, Peru’s anchoveta catch is one of the largest single-species fisheries in the world, supplying much of the planet’s fishmeal and fish oil. When a strong El Niño arrives, that fishery can virtually vanish. During the 1982–83 event, catches fell to near zero and the anchoveta biomass hit the lowest level ever recorded at the time. The 1997–98 event was similarly devastating: estimated biomass plunged from about 5.8 million tonnes to a minimum of 1.2 million tonnes, and the remaining fish crowded closer to shore, making them harder for fishing fleets to reach.
5ICES Journal of Marine Science. Phenological mismatch contributes to anchoveta landings collapse under El Niño and climate change in the Peruvian upwelling systemPart of the collapse traces directly to the nutrient and plankton changes described above. But recent research highlights another layer: a timing mismatch between when anchoveta eggs hatch and when food is available for the larvae. Under normal conditions, water temperatures reach the range that triggers optimal egg hatching in roughly February, coinciding with peak microplankton concentrations. During the 1982–83 and 1997–98 events, abnormal warming pushed temperatures well above the threshold for proper larval development throughout spring. By the time waters cooled enough, it was the austral winter, and the plankton the larvae needed had already declined sharply. That mismatch between hatch timing and food availability compounds the simple loss of nutrients, hitting the next generation of anchoveta before it even enters the fishery.
6ICES Journal of Marine Science. Phenological mismatch contributes to anchoveta landings collapse under El Niño and climate change in the Peruvian upwelling systemTuna on the Move
While anchoveta populations shrink in place, tropical tunas respond to El Niño by moving, sometimes thousands of kilometers. Skipjack tuna, the species that fills most of the world’s canned tuna, is closely tied to the warm pool in the western Pacific. During El Niño, that warm pool slides eastward, and the skipjack go with it.
7Nature. El Nino Southern Oscillation and tuna in the Western PacificFor Pacific Island nations that depend on licensing fees from distant-water tuna fleets, this is not a minor adjustment. When fish accumulation shifts toward the central and eastern Pacific during El Niño, catch rates drop in the western Pacific fishing grounds that small island economies count on. La Niña reverses the pattern, concentrating fish back in the west.
8IOP Conference Series: Earth and Environmental Science. Impact of ENSO-Driven Warm Pool Shifts on Skipjack Tuna (Katsuwonus pelamis) CPUE in the Pacific OceanThis displacement creates winners and losers among fishing nations. Fleets based in the central Pacific may see bumper seasons, while those in the far western Pacific struggle. The fish are not necessarily more or less abundant globally; they are just somewhere else. For fishers tied to a particular port or exclusive economic zone, that distinction is cold comfort.
Squid Fisheries and Shifting Migration Routes
Jumbo flying squid, one of the most commercially important cephalopod species in the eastern Pacific, are acutely sensitive to El Niño. Off the coast of Peru, El Niño weakens the upwelling-driven processes that concentrate chlorophyll and the prey squid feed on, leading to notable drops in catch rates.
9Journal of Marine Science and Engineering. The Impact of Ekman Pumping and Transport on Dosidicus gigas (Jumbo Flying Squid) Fishing Ground by Chinese Jiggers off the Coast of PeruThe effects run deeper than reduced abundance in traditional fishing grounds. Strong El Niño events reshape the squid’s entire migration and reproductive cycle. Research tracking their movements found that reproductive migratory distances during strong El Niño phases averaged only about 434 kilometers, compared with roughly 894 kilometers during La Niña periods. In other words, the squid travel barely half the distance they normally would. Moderate El Niño events produce an intermediate compression of about 620 kilometers.
10Communications Earth & Environment. Strong El Niño events reshapes migration routes and reproductive phenology of jumbo squid (Dosidicus gigas)For squid fishing fleets, this means the animals are not where they are expected to be, and the fishery’s geographic footprint shrinks along with the squid’s range. Combined with the drop in productivity from reduced upwelling, El Niño years tend to be bad years for squid jiggers operating off South America.
Unfamiliar Fish in Temperate Waters
While tropical and subtropical species contract or shift within their usual range, El Niño also pushes warm-water species poleward into regions where they are rarely seen. Off Southern California, El Niño events drive tropical water northward, and the local fish community changes substantially. Species that normally live off Baja California or further south show up along the coast, sometimes in numbers large enough to attract recreational and commercial attention.
11Estuarine, Coastal and Shelf Science. Unusual occurrences of fishes in the Southern California Current System during the warm water period of 2014–2018This pattern plays out along other coastlines too. Australian waters, the coasts of Japan, and parts of South America all see unusual visitors during strong events. For local fishers, these arrivals can be confusing: unfamiliar species may lack established markets, gear may be wrong for catching them, and regulations may not cover them. Meanwhile, the cool-water species that local fisheries are built around may have retreated north or into deeper water.
Coral Reef Fisheries and Habitat Loss
El Niño’s best-known effect on coral reefs is bleaching, and the consequences for reef-dependent fisheries build over time. The immediate die-off of coral itself threatens only a small fraction of the species fishers typically target: about 6 percent of targeted reef fish are directly susceptible to coral mortality. The bigger problem is what comes after. As dead coral skeletons erode and the structural complexity of the reef degrades, an estimated 56 percent of fish species that fishers pursue lose the habitat they depend on for shelter and feeding.
12Journal of Applied Ecology. Gear‐based fisheries management as a potential adaptive response to climate change and coral mortalityThis delayed cascade means that the worst impacts on reef fisheries may not be felt during the El Niño event itself but in the years that follow, as habitat deteriorates. Communities in the Indo-Pacific and Caribbean that rely on reef fish for protein and income face a creeping decline rather than a sudden crash, which can make the problem harder to recognize and respond to.
Freshwater Fishing During El Niño Droughts
El Niño is not strictly an ocean phenomenon. The atmospheric circulation changes it triggers bring drought to large parts of Southeast Asia, northern South America, and southern Africa. Freshwater fisheries feel this in two ways: lower water levels reduce habitat for fish, and fish behavior changes in ways that make them harder to catch.
In Suriname, catches of lagoon fish track rainfall closely, declining when El Niño–driven dry spells reduce freshwater inflow.
13Environmental Biology of Fishes. Effects of El Niño-related Drought on Freshwater and Brackish-water Fishes in Suriname, South AmericaIn Borneo, a study during an extreme El Niño drought found that a common freshwater species did not actually decline in overall density or biomass, but the fish became much more difficult to catch. For rural communities relying on those fish as a food source, the practical effect was the same as a population crash: less fish on the plate.
14Environmental Research Letters. Resilience of tropical, freshwater fish (Nematabramis everetti) populations to severe drought over a land-use gradient in BorneoThis distinction between actual fish abundance and catchability matters for management. If drought-stressed communities respond to low catches by assuming the fish population has collapsed and abandon sustainable practices, or if they intensify effort with destructive methods to compensate, the real decline can follow the perceived one.
Harmful Algal Blooms
Warmer water during El Niño does not just reduce beneficial plankton; it can also fuel harmful algal blooms. Strong events have been linked to catastrophic blooms in geographically distinct regions, producing toxins that contaminate shellfish, kill fish, and shut down fisheries for safety reasons. These blooms can devastate aquaculture operations and coastal fisheries simultaneously, and the economic damage extends beyond the fishing season into tourism and public health costs.
15Harmful Algae. Pelagic harmful algal blooms and climate change: Lessons from nature’s experiments with extremesThe connection between El Niño and harmful blooms is not automatic. Blooms require the right combination of temperature, nutrients, stratification, and sometimes freshwater runoff from storm events. But strong El Niño events load the dice, creating conditions that favor the harmful species over the ones that form the base of a healthy food web.
Economic Ripple Effects Beyond the Dock
When the Peruvian anchoveta fishery contracts, the effects travel far from South America. Anchoveta is the primary raw material for fishmeal, which is a key ingredient in feed for farmed salmon, shrimp, and other aquaculture species worldwide. El Niño–driven reductions in anchovy production tighten global fishmeal supply, driving up prices. Aquaculture operations in Southeast Asia, Europe, and elsewhere feel the squeeze through higher feed costs, which can make farming certain species unprofitable in bad years.
16Frontiers in Sustainable Food Systems. Implications of feed and seed costs in Asian seabass mariculture in the face of climate changeAt the local level, small-scale fishing communities bear a disproportionate share of the pain. Research on the Galápagos Islands documents a pattern that repeats across El Niño–affected regions: reduced landings, longer search times as fishers range further to find fish, higher fuel and operating costs, and increased livelihood insecurity.
17Ocean & Coastal Management. An overview of social-ecological impacts of the El Niño-Southern Oscillation and climate change on Galapagos small-scale fisheriesFor artisanal fishers without the capital to switch gear, travel to new grounds, or wait out a bad season, El Niño can push households into debt or force people out of fishing entirely. Some turn to alternative livelihoods like agriculture or construction work, but in remote coastal communities the options are limited. The social toll is hardest to quantify and easiest to overlook in discussions that focus on catch statistics.
Can Forecasts Help Fisheries Prepare?
Modern climate forecasting can predict El Niño events several months in advance, and there is real economic value in using those forecasts for fisheries management. A study modeling Pacific salmon management found that a perfect El Niño forecast would produce an annual welfare gain of roughly one million dollars for a single fishery. Even imperfect forecasts yielded measurable benefits. The study also suggested that the best strategy under uncertainty is a conservative one: lower harvests, higher wild fish escapement, and fewer hatchery releases than would be optimal if managers could ignore El Niño altogether.
18American Journal of Agricultural Economics. The Value of El Niño Forecasts in the Management of Salmon: A Stochastic Dynamic AssessmentIn practice, many fisheries management systems are still reactive rather than anticipatory. Peru adjusts its anchoveta quotas based on acoustic surveys of current biomass, which helps but does not prevent the economic shock. Tuna management bodies set catch limits years in advance and struggle to account for interannual shifts driven by climate variability. The gap between what forecasts could enable and what management systems actually do with that information remains wide.
Thousands of Years of El Niño and Fishing
El Niño’s disruption of fishing is not a modern discovery. Archaeological sites along the Peruvian coast preserve evidence of different El Niño “flavors” stretching back roughly 11,000 years, including eastern Pacific events, central Pacific events, and coastal events. Climate proxy data from these sites show that coastal communities have been coping with El Niño–driven fishery disruptions for millennia, long before anyone named the phenomenon or understood its mechanics.
19PubMed Central. Archaeological climate proxies and the complexities of reconstructing Holocene El Niño in coastal PeruWhat the archaeological record shows is that ancient Peruvian fishing communities were not passive victims. Shifts in the species composition of fish remains at archaeological sites suggest that people adapted by targeting different species when their usual catch disappeared. Some sites show increased reliance on shellfish or terrestrial foods during El Niño periods. These adaptations have echoes in what modern small-scale fishers do: switching target species, shifting to nearshore gathering, or temporarily leaving the fishery. The difference today is that industrial-scale fisheries and global supply chains amplify both the economic damage and the recovery challenge in ways that a village-level fishery never had to face.