Kenya is putting its health system on high alert ahead of the expected 2026/2027 El Niño season, with the government rolling out measures to prevent disease outbreaks, protect vulnerable communities and keep essential health services running in areas likely to be hit by floods.
The Ministry of Health said Friday that it had activated a Health Sector El Niño Contingency Plan to guide preparations across the country, bringing together national and county governments, emergency agencies, humanitarian organisations and development partners.
The plan is focused on preparing for health emergencies that could arise from heavy rains, flooding, displacement and damage to health infrastructure and other essential services.
A major concern is the possible rise in water- and food-borne diseases, including cholera, typhoid, dysentery, hepatitis A and other diarrhoeal illnesses. Such diseases can spread when floods contaminate water sources and damage sanitation systems.
“The Health Sector El Niño Contingency Plan provides a common framework for national and county governments, emergency agencies, humanitarian organisations and development partners to anticipate, prevent, detect and respond rapidly to flood-related health emergencies,” the Ministry of Health said.
The preparations come days after Deputy President Kithure Kindiki directed counties to activate their disaster response systems ahead of the October-December rainy season.
Speaking during the 30th Ordinary Session of the Intergovernmental Budget and Economic Council on August 24, Kindiki said 18 counties, as well as Nairobi, Mombasa and Kisumu, had been identified as being at higher risk of flooding, landslides, disease outbreaks, displacement and damage to infrastructure.
He urged counties to act before the rains intensify by clearing drainage systems, mapping vulnerable communities, stocking essential supplies and improving the readiness of emergency response teams.
“I urge all county governments to urgently activate their disaster preparedness and response plans, clear and maintain drainage systems, identify and protect vulnerable communities, pre-position essential supplies, strengthen emergency response teams and coordinate closely with national agencies,” the DP stated.
Kindiki has also called for food and non-food relief supplies to be moved closer to communities considered vulnerable before the rains arrive. He warned authorities against waiting for emergencies to happen before taking action.
The Deputy President said national authorities were holding regular meetings as they prepare for the expected weather conditions.
“We don’t want to be caught unawares in the situation that is ahead of us,” he warned.
The heightened preparations follow climate projections showing a higher possibility of El Niño conditions towards the end of 2026. The Kenya Meteorological Department's 2025 State of the Climate report placed the likelihood of El Niño conditions between June and December at 58-61 percent, warning that the phenomenon could strengthen the October-November-December short rains and raise flooding risks in vulnerable river basins.
The Health Ministry is now working to strengthen disease surveillance, with county health teams expected to investigate alerts, send rapid-response teams to affected areas and use mobile data collection and daily situation reports to support faster decisions.
Laboratory capacity is also being strengthened through improved sample-referral networks, additional reagents and rapid diagnostic tests for priority diseases such as cholera and typhoid. Mobile laboratories will be deployed in areas where they are needed.
The government is also procuring and pre-positioning essential medicines, laboratory supplies, infection-prevention materials, nutrition commodities and emergency kits at regional, county and health facility levels.
Alternative last-mile delivery arrangements are being prepared for communities that could be cut off by floods, to help ensure critical medical supplies continue reaching affected areas.
Water, sanitation and hygiene measures will include monitoring water quality, chlorinating and disinfecting contaminated sources, providing household water-treatment supplies, deploying mobile treatment units and setting up handwashing facilities and mobile toilets.
At the county level, authorities are strengthening contingency plans while preparing ambulances, evacuation arrangements, temporary and mobile clinics, backup power systems and referral networks to help maintain healthcare services during emergencies.
The Ministry said particular attention would be given to pregnant women, children, older people, people living with chronic conditions and other vulnerable groups.
Community Health Promoters will also support preparedness at household level by educating residents on safe water treatment, food hygiene and the need to seek medical care early when symptoms develop.
The Ministry has urged people living in flood-prone areas to treat drinking water, maintain proper hand hygiene and avoid consuming food that has come into contact with floodwater.
Those who develop persistent fever, severe headache, abdominal pain, vomiting, profuse watery diarrhoea, blood in stool, unusual weakness or signs of dehydration have been advised to seek medical attention without delay.
The government is coordinating the preparedness effort with the Kenya Red Cross Society, National Disaster Operations Centre, KEMSA, KEMRI and international partners.
The Ministry of Health said it would continue tracking weather conditions and disease trends and adjust its preparedness measures as the situation changes.