Kenya Steps Up Health Defences as El Niño Raises Flood Fears

The warning comes only months after Kenya experienced widespread flooding during the March–May 2026 long rains.

Kenya is strengthening its health preparedness ahead of the anticipated 2026/2027 El Niño season, as forecasts suggest that parts of eastern Africa may receive heavier-than-normal rainfall between October and December. The expected combination of strong El Niño conditions and a positive Indian Ocean Dipole could bring wetter weather to northern Kenya and neighbouring countries, raising concerns about flooding, disease outbreaks and disruption to essential health services.

Recent floods reveal the scale of the danger

The warning comes only months after Kenya experienced widespread flooding during the March–May 2026 long rains. By 3 May, floods had reached 27 counties, killed 122 people and affected 42,259 residents, while damaged roads, bridges, water networks and electricity infrastructure made it difficult for many communities to reach health facilities or obtain basic services.

Eastern Africa has faced similarly destructive weather before. Strong El Niño and positive Indian Ocean Dipole conditions in 1997 and 2019 were followed by extensive flooding across the region, bringing displacement, damaged livelihoods and serious public health consequences. Somalia, eastern and southern Ethiopia, northern Kenya, Uganda, Rwanda and Burundi are among the areas expected to experience above-normal rainfall during the coming season.

Contaminated water could drive disease outbreaks

For families living in flood-prone settlements, unusually heavy rain can quickly become a health emergency. Floodwater may enter wells, boreholes and household water supplies, while overflowing toilets and damaged sanitation systems can spread dangerous bacteria and viruses through communities.

These conditions increase the threat of cholera, typhoid, dysentery, hepatitis A and other diarrhoeal illnesses, particularly among children, older people and families without access to safe water. Flooded roads can delay ambulances, prevent patients from collecting medicines and interrupt routine services such as vaccinations, maternal care and treatment for chronic conditions.

Health facilities may also face overcrowding, damaged equipment or shortages of medicines and clean water at the moment communities need them most. Preparing clinics and response teams before the rains arrive could reduce preventable illness and help services continue during severe weather.

Kenya activates coordinated health contingency plan

The Ministry of Health has activated its Health Sector El Niño Contingency Plan, bringing together national and county governments, emergency agencies, humanitarian organisations and development partners. The plan covers disease surveillance and early warning, laboratory readiness, emergency response capacity, safe water and sanitation, public risk communication and the continuation of essential healthcare.

The World Health Organization is supporting the Ministry of Health and the Kenya National Public Health Institute as planning and risk assessments continue. This work is expected to help officials identify vulnerable locations, monitor emerging health threats and position necessary supplies and response teams.

"The experience of the long rains earlier this year provides important lessons for preparing health services and communities before the next rainy season," said Dr Neema Rusibamayila Kimambo, WHO Representative to Kenya.

For households, early information about evacuation routes, safe drinking water, emergency contacts and nearby health facilities could make a major difference when flooding begins. Kenya's preparations recognise that extreme rainfall is not only a weather concern but a public health challenge requiring action before roads disappear beneath water and disease starts spreading.