Understanding El Niño: The ocean pattern reshaping East Africa's rainy season

Every few years, a shift beneath the surface of the tropical Pacific Ocean sets off a chain reaction that reshapes weather patterns across the globe. 

This is El Niño, a natural climate pattern in which surface waters in the central and eastern Pacific warm well above average. 

Peruvian fishermen gave the phenomenon its name, "El Niño" (the Christ Child), after noticing a warm current that disrupted fish catches, typically appearing around Christmas time.

El Niño is one phase of a larger climate cycle called the El Niño-Southern Oscillation, or ENSO. This cycle oscillates between three states.

In normal, or "neutral," conditions, strong easterly trade winds push warm surface water westward across the Pacific, allowing cooler, nutrient-rich water to rise along South America's coast. 

During El Niño, those trade winds weaken or even reverse, letting warm water pool in the central and eastern Pacific instead.

The opposite phase, La Niña, brings intensified trade winds and unusually cool ocean surface temperatures in the same region.

These shifts in ocean temperature are confined to the Pacific Ocean alone. Because the ocean and atmosphere are tightly linked, changes in sea-surface temperature alter where clouds form, where rain falls, and how jet streams behave, sending ripples through weather systems worldwide. 

An El Niño episode typically builds over several months; it peaks between November and February, and can last up to 18 months before fading back to neutral; La Niña episodes, by contrast, can persist for up to three years.

A strong El Niño is building in 2026

According to the U.S. Climate Prediction Center has forecasted the awaited El-Nino a chance of being very strong during the last months of 2026 and into early 2027, with a strength above 90 per cent. 

The World Meteorological Organization (WMO) has confirmed this trajectory, reporting that El Niño is expected to intensify into a strong event during the August-October 2026 season, its effects amplified by exceptionally warm global oceans and the likely emergence of a positive Indian Ocean Dipole, which, is a separate but related pattern of warming in the western Indian Ocean that tends to reinforce El Niño's rainfall effects over East Africa. 

Some researchers go further, projecting the event could reach "super" strength. One recent academic assessment estimated a 63 to 65 per cent chance of the El Niño reaching super-strength between October 2026 and February 2027, which would place it among the most powerful on record, alongside the 1997-98 and 2015-16 events. 

The Horn of Africa: a region of contrasts

For most of the world, El Niño's arrival is unambiguously bad news; it might mean a drought in Australia and Indonesia, and flooding in parts of South America.

East Africa's relationship with the pattern is more complicated, and 2026 is illustrating why.

The region has effectively faced two seasons in one year. Earlier in 2026, forecasters warned of a drier-than-normal June-to-September season across northern and western parts of the Greater Horn of Africa. 

IGAD’s Climate Prediction and Applications Center (ICPAC) outlook found the highest likelihood of below-normal rainfall over central, northeastern and northwestern Ethiopia, southern Sudan, and northern Uganda, with probabilities exceeding 60 per cent and peaking at 80 percent in northeastern Ethiopia. 

That dry spell squeezed water resources, agriculture, and pastoral livelihoods in a season that normally supplies more than half of the region's annual rainfall. 

Now, as El Niño strengthens further, the outlook has flipped for the region's second rainy season. In its most recent forecast, issued at the Greater Horn of Africa Climate Outlook Forum in Kigali on 17-18 August, ICPAC found an increased likelihood of wetter-than-normal conditions across the Greater Horn of Africa in the October-to-December period. 

This rainy season, known locally as the "short rains," is critical: it supplies up to 70 per cent of annual rainfall in parts of Ethiopia, Kenya and Somalia, and up to 40 per cent in parts of Rwanda, Burundi, Tanzania and Uganda. 

How much rain, and where?

Forecasters are using a suite of climate models to estimate probabilities down to the sub-regional level. Some zones face particularly high odds of a very wet season. 

ICPAC's outlook shows rainfall probability zones with as much as a 90 per cent chance of above-normal rainfall in parts of the region, with a high probability that many areas will exceed 300 millimeters of rainfall over the season. 

In the wettest zones, the numbers climb higher still: forecasters say there is a high chance of seasonal rainfall exceeding 400 millimeters in parts of central and southern Somalia, central Kenya, the Lake Victoria Basin, Burundi, western Rwanda and western Tanzania. 

September itself is expected to remain relatively dry, with the bulk of the rainfall increase arriving later in the season. 

Climate scientists are drawing comparisons to two previous strong El Niño years in 1997 and 2023, as rough guides for what could unfold, while cautioning that the current seasonal forecast, not historical analogues, should guide planning decisions. 

The 1997-98 event remains the region's benchmark flood disaster: months of excessive rain across Kenya, Somalia and Ethiopia displaced hundreds of thousands of people, destroyed infrastructure, and triggered one of the largest recorded outbreaks of Rift Valley fever, a mosquito- and livestock-borne disease.

Infrastructure, health and humanitarian stakes

The dual nature of El Niño's impact on East Africa- welcome relief for drought-stressed pastures and reservoirs, but a serious flood and disease hazard when rain arrives in torrents — is already shaping government responses.

In Rwanda, authorities are stepping up preparations for floods and landslides, a concern sharpened by a recent flood disaster in the country that killed 130 people and swept away more than 5,000 houses.

Regional officials are urging governments to strengthen early warning systems and protect vulnerable communities in the months before the rains intensify.

Heavy, concentrated rainfall on already degraded land raises the risk of flash floods, landslides, and damage to roads, bridges and housing, disrupting transport and market access across the region. 

On the health front, standing water and flooding typically drive up cases of waterborne diseases such as cholera, along with mosquito-borne illnesses like malaria and Rift Valley fever, a pattern that health authorities should watch closely given the scale of the 1997 outbreak. 

Regional forecasts are explicitly designed to feed into planning for health campaigns, crop and irrigation decisions, and disaster management, precisely because of these cascading risks.

The economic stakes are significant. Millions of people across the region depend directly on seasonal rainfall for food production, water access, and livelihoods, and food insecurity in the Horn of Africa was already severe going into this El Niño episode, with tens of millions of people classified as facing high levels of acute food insecurity. 

A wet season could replenish water sources and improve rangeland conditions for herders recovering from earlier drought, but only if the rains arrive at a manageable pace, rather than in the destructive deluges of 1997.

What comes next

The WMO is due to issue its next global El Niño update on 3 September, which will offer an updated, authoritative read on the event's strength heading into the peak of the short rains. 

Regional meteorological services across the Greater Horn of Africa say they will continue to refine and localize these forecasts as October approaches, tracking river levels on waterways such as the Tana, Juba and Shabelle once the rains begin, a signal, alongside the strength of the Pacific signal itself, of how hard this El Niño will ultimately hit the region.