The Ministry of Health has warned of an increase in food-borne illnesses as Kenya prepares for El Niño-enhanced rains expected to bring flooding, water contamination and food spoilage.
In a food safety advisory issued on Monday, the ministry said experience from previous El Niño seasons showed that heavy rains, flooding and high humidity could lead to a sharp rise in illnesses such as cholera, typhoid and aflatoxin poisoning.
It urged households, food vendors and estates to prepare before the rains begin, warning that “prevention is better than cure”.
The ministry said flood water was likely to mix with sewage and contaminate shallow wells, boreholes and piped water, particularly in low-lying areas.
“Flood water is likely to mix with sewage, contaminating shallow wells, boreholes and piped water, especially in low-lying areas,” it said.
Households have been advised to stock Water Guard and chlorine tablets, while cleaning and covering water storage tanks and jerry cans.
The ministry also wants families to keep a separate clean and covered container for drinking water.
It warned that high humidity could accelerate mould growth on maize, peanuts and animal feeds, increasing the risk of aflatoxin contamination.
Kenyans have been advised to ensure maize flour, maize grains, groundnuts and beans are completely dry and stored off the floor on pallets or shelves in airtight containers.
Those with old cereal stocks from the previous season have been urged to sun-dry them before the rains begin.
The ministry also expects power outages to disrupt cold-chain storage, potentially causing milk, meat and leftovers kept in fridges and freezers to spoil.
Major markets could also flood, exposing food to “dirty water, mud and flies”.
Food businesses and informal traders have been advised to raise food off the ground, keep it covered and improve drainage around their stalls. The ministry said county inspections would increase and urged food handlers to have their medical certificates ready.
Families with children under five and elderly people have also been urged to reinforce hygiene, including teaching children to wash their hands with soap before eating.
Community Health Promoters and Nyumba Kumi groups have been asked to organise drainage clean-ups, unclog trenches and sensitise communities on boiling water before the rains.
The advisory comes as Kenya braces for the October-December rainy season, with regional forecasts pointing to wetter-than-normal conditions across much of the Greater Horn of Africa.
According to the World Meteorological Organization (WMO),the Greater Horn of Africa is expected to be wetter than usual in the final quarter of 2026 as El Niño strengthens.
The organization said October to December is a critical rainfall period for Kenya and neighbouring countries, with an increased likelihood of wetter-than-normal conditions and a heightened risk of flooding and damage to infrastructure.
The Kenya Meteorological Service Authority had also forecast above-average rainfall in several parts of the country during the period with the Kenyan government identifying 18 counties considered highly vulnerable to El Niño-related impacts.
They include Tana River, Kilifi, Lamu, Mombasa and Kwale in the Coast; Kisumu, Busia, Siaya, Homa Bay and Migori in the Lake Basin; Turkana, Baringo, West Pokot and Narok in the Rift Valley; and Garissa, Wajir and Mandera in North Eastern. Nairobi has also been classified as a high-risk urban centre, alongside Mombasa and Kisumu.
The risks identified across the counties include flooding, landslides, infrastructure damage, displacement, disease outbreaks, drought, livestock losses and food insecurity.