Nairobi — The Ministry of Health has activated its El Niño preparedness plan in 18 high-risk counties as Kenya braces for heavy rains expected during the October-December season, with officials warning of increased flooding, displacement and outbreaks of waterborne and vector-borne diseases.
Public Health and Professional Standards Principal Secretary Mary Muthoni said the ministry was seeking support from development and health partners to strengthen the government's response and ensure essential services reach communities likely to be affected.
Speaking on Wednesday during a health partners' engagement ahead of the Kenya Public Health International Conference (KEPHIC) 2026, Ms Muthoni said Kenya had learnt important lessons from previous El Niño-related disasters and was better prepared to respond to the expected rains.
"We have experienced El Niño before, and we have taken time to learn from past disasters and build on the challenges we faced so that we can better mitigate its effects," Muthoni said.
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The ministry is seeking assistance for temporary medical structures, emergency medical services, health promotion campaigns, nutritional assessments, safe water and sanitation interventions, logistics, protection of critical health infrastructure and medical supplies.
The government has identified 18 counties as particularly vulnerable to the effects of the anticipated rains. They include areas in the Coast, Lake Basin, Rift Valley and North Eastern regions, with Nairobi, Mombasa and Kisumu also identified as high-risk urban centres.
In the Coast region, Tana River, Kilifi, Lamu, Mombasa and Kwale face risks including flooding, storm surges, coastal erosion and infrastructure damage. In the Lake Basin, Kisumu, Busia, Siaya, Homa Bay and Migori are at risk of flooding, landslides, disease outbreaks and displacement.
The ministry is particularly concerned about the health consequences of flooding, which can contaminate water sources and overwhelm sanitation systems, increasing the spread of diseases such as cholera, typhoid, dysentery and other water- and food-borne illnesses. Heavy rains and stagnant water can also create breeding grounds for mosquitoes, raising the risk of malaria and other vector-borne diseases.
The government is also planning to distribute 10 million treated mosquito nets from November, targeting more than four million people considered vulnerable to malaria as part of measures to reduce the health impact of the rains.
The warning comes after Kenya suffered extensive flooding during the 2023 El Niño season. While the Health Ministry says 43 counties were affected, climate and health assessments show the scale of the disaster, with more than 750,000 people affected by floods between October and December 2023. The floods caused deaths, displacement and damage to homes, roads, farms and other critical infrastructure.
The experience also exposed the vulnerability of the health system. During the wider flooding crisis, dozens of health facilities were affected, while contaminated water contributed to outbreaks of diseases including cholera. WHO reported that by late November 2023, 33 counties had experienced above-normal rainfall, with more than 93,000 households affected and 120 deaths reported at the time.
The Ministry of Health has previously warned that El Niño-related flooding can disrupt access to healthcare, cut off roads and isolate communities, making it difficult for medical teams and supplies to reach affected areas. The ministry has therefore been strengthening disease surveillance, emergency response teams and coordination with county governments and humanitarian partners.
The latest preparations come as Kenya also recovers from widespread flooding experienced during the March-May 2026 long rains. The World Health Organisation said the anticipated 2026/27 El Niño season, combined with a positive Indian Ocean Dipole, could bring wetter-than-normal conditions to parts of East Africa between October and December.
The government has consequently stepped up its wider disaster preparedness, including crisis communication, with officials seeking to ensure weather warnings translate into timely action at community level.
Ms Muthoni said the health response could not be handled by the government alone and urged partners to complement State efforts, particularly in areas where flooding could overwhelm existing facilities and infrastructure.
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She said the planned KEPHIC conference, scheduled for October 27-29, would provide an opportunity for health-sector players to examine lessons from previous emergencies and strengthen partnerships around preparedness and response.
The PS also disclosed that the State Department for Public Health had prepared a Cabinet memorandum seeking approval for the introduction of a monthly national cleanliness day, modelled on Rwanda's community-cleaning programme.
The proposed initiative would give Kenyans a designated day each month to clean their estates and surrounding areas, an intervention the ministry believes could help reduce waste accumulation and blocked drainage systems ahead of the heavy rains.
With forecasts pointing to potentially wetter-than-normal conditions, health officials are urging early preparation rather than waiting for flooding to occur before response measures are activated.
