El Niño 2026: How warm Pacific waters flood, make Kenyans sick

Nairobi · 29 September 2026

On 10 September, forecasters at the US Climate Prediction Center, part of the National Oceanic and Atmospheric Administration (NOAA), quantified what Kenyan disaster planners had feared all year. They gave better than 90 per cent odds that the El Niño building in the Pacific will be very strong by December, and 75 per cent odds that between October and December it will surpass every El Niño recorded since 1950.

Eleven days later, Columbia University scientists reported that Niño 3.4, the band of equatorial sea that serves as El Niño’s pulse, had warmed to three degrees Celsius above normal. All 22 computer models they track agreed: the event is still strengthening.

Draw a line from Nairobi through the centre of the Earth and it emerges inside Niño 3.4.

The engine room: How El Niño forms

In an ordinary year, the Pacific is not level. Trade winds push sun-warmed surface water west, the way wind drives water to one end of a dam, until the sea near Indonesia stands about half a metre higher than off Ecuador. This warm pool, close to 30 degrees Celsius, heats the air above it, and rain falls on Indonesia and northern Australia.

Off South America, cold, nutrient-rich water rises to fill the gap, feeding some of the world’s richest fisheries.

El Niño starts when the trade winds weaken. Westerly gusts break through, and the warm water slides east as a hidden swell beneath the surface, a Kelvin wave, taking about two months to cross.

At South America it caps the cold water below. The central and eastern Pacific warms by one to three degrees, and the rain follows the warm water east. NOAA’s 10 September update found the eastern Pacific surface more than three degrees above normal, and deeper water more than 10.

Air rising in one part of the tropics must sink elsewhere, and where it sinks, weather turns dry. When El Niño pushes the rising air east, the whole tropical loop shifts with it.

That is how a distant ocean reaches Kenya.

El Niño: Name linked to Christmas and why it returns every 2 to 7 years

Fishermen named it long before scientists understood it. Centuries ago, in Peru and Ecuador, they noticed that in some years the sea warmed around December, fish vanished and rain fell on desert shores. They called the current El Niño, the boy child, after the Christ child whose birthday it seemed to mark.

In the 1920s Gilbert Walker, a British scientist trying to forecast India’s monsoon, found a see-saw in air pressure across the Pacific and named it the Southern Oscillation.

In 1969 Jacob Bjerknes showed that the warming sea and shifting winds were one machine, now called ENSO. El Niño is its warm phase; La Niña its cold.

Climate change did not create El Niño. Yearly bands in corals from the Pacific’s Line Islands, like tree rings, trace its rhythm back thousands of years. What has changed is the baseline: each event now heats an ocean and atmosphere already warmer than ever recorded.

El Niño returns every two to seven years. It typically forms between April and June and peaks between October and February, exactly when Kenya’s short rains fall.

That last detail is the one that matters in Kenya, because October to December is the short rains.

Dry air: El Niño loosens it, unleashing short, heavier rains across Kenya

Scientists call these long-distance links teleconnections. The Pacific does not send rain to Kenya. It reshuffles the atmosphere, and the atmosphere reshuffles the rain.

Kenya lies on the equator, like the Amazon, yet most of it is dry. Across the Indian Ocean, air normally rises near Indonesia and sinks over the Horn of Africa. Sinking air is dry and acts like a lid on clouds, which is why Mandera, Wajir and Garissa stay parched.

El Niño loosens that lid, so the short rains tend to be heavier across Kenya, southern Somalia, Uganda and northern Tanzania.

Elsewhere, it works in reverse. In early 2024, El Niño drought drove Zambia, Zimbabwe and Malawi to declare national disasters; in 2015, failed rains left over 10 million Ethiopians needing food aid.

One ocean, one event, a continent split between flood and drought.

East Africa has a second driver, closer to home: the Indian Ocean Dipole. When the sea off East Africa runs warmer than usual and the sea near Indonesia cooler, the dipole is positive. Warmer water gives off more moisture, which winds carry onto the coast. Australia’s Bureau of Meteorology put the dipole at 0.65 degrees in the week to 13 September, past the positive threshold, and expects it to hold.

El Niño does not, by itself, decide how much rain falls in Kenya

Stanley Kinyua of the Kenya Meteorological Department in Narok explained in August that this season would hinge largely on the dipole, which can amplify El Niño’s effect over East Africa or cancel it out.

History agrees. In 1997, a very strong El Niño teamed up with an exceptionally strong positive dipole, and the short rains came in at about twice their usual level. In 2015, the Pacific ran hotter but the dipole was weak: rains were about 50 per cent above normal but patchy, missing much of eastern and central Kenya. In 2019, with barely an El Niño, Kenya flooded because the dipole ran high.

This year, both are moving together. The forecasting firm Climate Impact Company noted on 21 September that among recent positive dipoles of similar strength, only two came with an El Niño: 1997 and 2023.

Both of those seasons are written into Kenya’s disaster records.

The season ahead: El Niño’s impact in Kenya

Across much of the highlands, the October to December short rains are Kenya’s lesser season. In Garissa, Wajir, Mandera, Marsabit, Isiolo, Kitui and much of the southeast, they bring more than 40 per cent of the year’s rain. Normally, that rain regrows pasture and refills water pans. In an El Niño year, it floods.

The Kenya Meteorological Department outlook, issued on 26 August, warns of long wet spells and occasional isolated storms. Western Kenya, the Rift Valley and the Lake Victoria basin, including Nandi, Bungoma, Trans Nzoia, Kisumu and Kericho, should stay wet into January 2027. Elsewhere, the rains should begin in the second or third week of October.

The World Bank priced the 1997-98 floods at Ksh70 billion; with the La Niña drought that followed, the 1997 to 2000 cycle cost about Ksh290 billion, close to 14 per cent of the economy’s output in those years. The International Monetary Fund (IMF) estimates that floods cost Kenya about one shilling in every 18 it earns, once every seven years.

The National Disaster Operations Centre (NDOC) rates 18 counties as high risk. A joint assessment by the Food and Agriculture Organization (FAO), the World Food Programme and the Kenya Meteorological Service Authority (KMSA) names 23. Together they cover 28 of Kenya’s 47 counties, with 13 on both lists. For Garissa, Wajir and Mandera, NDOC flags drought, water shortages and livestock deaths as well as floods.

In the northeast the danger in an El Niño year can come from both ends of the season.

Echoes of the past: What Kenya already knows about El Niño

The benchmark for East African floods is 1961, a year with no El Niño. A warm Indian Ocean alone unleashed rains so extreme that when the World Health Organization later reviewed the 1997 floods, 1961 was its only comparison.

In 1997, the Indian Ocean had help from a very strong El Niño. Rain fell from May until February 1998, the heaviest in three decades on the coast and in the northeast. Between 1,781 and 2,000 people died, about 250,000 lost their homes, and damage reached roughly a billion dollars.

In 2006-07, a much milder El Niño sparked Kenya’s worst Rift Valley fever outbreak in a generation: 404 cases and 118 deaths by 25 January 2007. The size of an event does not predict its toll.

Then 2015-16, among the strongest El Niños recorded, taught Kenya to stop listening. Kenya braced and budgeted, but floods hit some counties and spared their neighbours.

El Niño loads the dice. It does not choose where they land.

When warnings came in 2023, many shrugged. They were wrong. At least 174 people died between October and December, some 546,000 were displaced or affected, and 180 camps went up. About 90 per cent of those affected lived in Mandera, Garissa, Tana River, Wajir, Isiolo and Meru.

The El Niño ended; the water did not. The 2024 long rains fell on sodden ground, killing 257 people and displacing 293,000 across 31 counties. On 29 April, a blocked railway culvert above Mai Mahiu burst, killing at least 52 people in minutes.

And 2026 began badly with no El Niño in sight. By early April, rains had killed 112 people, and by early May floods or landslides had hit 39 of Kenya’s 47 counties.

That is the ground the short rains are about to fall on.

Ground zero: Budalang’i in Busia sits on the floodplain of the River Nzoia

Kenya floods in four ways, the first the slowest. Budalang’i in Busia sits on the floodplain of the River Nzoia; the Kano Plains in Kisumu sit on the Nyando. Both are flat, crowded and flooded so often that their dykes have names. Here the water is patient and stays for weeks.

The second comes from far away. The Tana basin, Kilifi and Lamu are swamped by rain that fell days earlier on the Aberdares and Mount Kenya, arriving down a single river as a wall of water. In December 2023, Tana River County alone held 61 of Kenya’s 180 displacement camps.

The third sounds like a contradiction: Kenya’s driest counties are among its deadliest flood zones. In Mandera, Wajir, Garissa and Isiolo, sun-baked ground sheds rain, so one storm can turn a dry riverbed into a torrent overnight. ICPAC, the regional climate centre, gives this area a 90 per cent chance of above-normal rain.

The fourth killer is slope. In Murang’a, Elgeyo-Marakwet, Nandi and the Gusii highlands, soaked volcanic soil on steep hillsides can give way suddenly, often at night.

This season is forecast to bring all four kinds of flood.

The second wave: How El Niño kills when cameras are not rolling

Kenya counts El Niño’s dead twice. The first, of drownings, landslides and collapsed houses, comes within hours. The second takes weeks, is scattered across clinics, is rarely linked to the flood, and is bigger.

Floodwater lifts sewage from pit latrines into water people wade through, wash in and, when taps fail, drink. That is how cholera spreads. In Kenya’s last major outbreak, the WHO logged 8,926 cases and 145 deaths; the health ministry counted 12,120 cases by October, 1.7 per cent of them fatal. By June 2026, cholera had reached 39 of Kenya’s 47 counties.

Rift Valley fever is the most sinister. Mosquito eggs carrying it lie dormant in dry soil for years, then hatch together when low ground floods. In 1997-98, it killed an estimated 478 people in northern Kenya and southern Somalia.

Because its floods follow warm seas, outbreaks can be forecast from the ocean.

Malaria rises after the flood, when receding water leaves warm pools for mosquitoes. It hits hardest in the western highlands, where immunity is low. Kericho hospital records show epidemic years when half the local population caught malaria and it caused 32 per cent of hospital deaths.

All this assumes patients reach a clinic. In the 2023-24 floods, 63 facilities in 11 counties were damaged and 64 of 1,434 assessed were cut off by washed-out roads. A cholera patient who reaches treatment has less than a 1 per cent chance of dying. Untreated, up to half can die.

The difference is often a passable road.

Meanwhile, vaccinations stop, chronic patients run out of medicine, pregnant women miss check-ups and vaccine fridges fail. None of these deaths are counted as El Niño deaths. All of them are.

By the time most victims fall sick, the flood is over, reported and off the news.