Why El Niño is forecast to bring wetter short rains to Kenya, and what WHO says about disease after floods

Forecasters expect a wetter-than-normal October–December season across the Greater Horn of Africa as El Niño strengthens, with a high chance of more than 400 mm of rain in central Kenya. The World Health Organization (WHO) links heavy rain and flooding to Rift Valley fever and cholera, and a 2007 study tied El Niño rains to a malaria epidemic in north-west Tanzania.

The IGAD Climate Prediction and Applications Centre (ICPAC) said in its 18 August outlook that El Niño has developed and is expected to strengthen further this year, and that the Indian Ocean Dipole is also expected to be in its positive phase. "These conditions normally lead to enhanced rainfall over the region during the OND season," it said. The World Meteorological Organization (WMO) repeated the forecast after the regional forum held in Kigali on 17–18 August.

In a positive phase of the Indian Ocean Dipole, the sea surface near Java and Sumatra is cooler than normal and the western tropical Indian Ocean is warmer, Nat Johnson wrote on the US National Oceanic and Atmospheric Administration's Climate.gov site on 27 February 2020. He listed floods in eastern Africa among the usual results.

The two patterns are linked. During El Niño, Johnson wrote, winds near Indonesia blow from the south-east to the north-west, helping to bring cold water to the surface near Java and Sumatra and starting a positive dipole, as in the extreme event of 1997.

ICPAC named 1997 and 2023 as analogue years, when wetter-than-normal conditions were seen across much of the region in October–December. WHO's Rift Valley fever fact sheet, updated 20 December 2024, records a major outbreak in Kenya, Somalia and Tanzania in 1997–98 after El Niño and extensive flooding.

ICPAC and WMO say October–December supplies up to 70% of annual rainfall in parts of Ethiopia, Kenya and Somalia. They put the chance of more than 400 mm as high in central Kenya, the Lake Victoria Basin, parts of central to southern Somalia, Burundi, western Rwanda and western Tanzania. WMO, citing a report by the Food Security and Nutrition Working Group, says excessive rain raises flood risk and the risk of water- and vector-borne disease outbreaks.

On 5 October, The Star reported that the Kenya Meteorological Department expects light to moderate rain in parts of 47 counties, with isolated storms that could cause flash floods in parts of Mandera, Wajir, Marsabit, Tana River and Kilifi.

Cholera is caused by consuming food or water contaminated with the bacterium Vibrio cholerae, WHO says in its fact sheet of 29 September 2026. WHO links the disease to limited access to safe water and basic sanitation and to poor hygiene, which it says may be due to causes including conflict, population displacement and climate events such as cyclones, floods or drought. Access to safe water, basic sanitation and hygiene is essential to prevent cholera, WHO says, and most people can be treated successfully with prompt oral rehydration solution.

Rift Valley fever is a viral disease that mainly affects animals but can also infect people, WHO says. The virus was first identified in 1931 during an investigation into an epidemic among sheep in the Rift Valley of Kenya. Among animals it is spread mainly by the bite of infected mosquitoes, mostly Aedes species. Most human infections come from contact with the blood or organs of infected animals. WHO says that in East Africa outbreaks are closely associated with the heavy rainfall of the warm phase of the El Niño–Southern Oscillation.

Most human infections cause no symptoms or a mild illness with flu-like fever, muscle and joint pain and headache, WHO says. Symptoms usually last four to seven days, and a small percentage of patients develop a much more severe form of the disease. WHO advises people to wear protective equipment when handling sick animals, to cook animal products thoroughly and to prevent mosquito bites. Christopher Wanga, director in charge of livestock policy, research and regulations at the Ministry of Agriculture and Livestock Development, said, as quoted by The Star on 11 September: "With El Niño comes two areas of destabilisation. You are looking at the habitats for livestock being affected. We will have disease vectors." He also said: "We have continuous supplies of vaccines for Rift Valley fever."

Malaria mostly spreads to people through the bites of some infected female Anopheles mosquitoes, WHO says. In 2024 the WHO African Region was home to 95% of the world's malaria cases and 95% of malaria deaths. A 2007 study in Malaria Journal found that malaria incidence in Kagera region, north-west Tanzania, was positively correlated with rainfall in the October–March season, and linked heavy El Niño rains to the 1998 epidemic.