# What happened Kenya's Meteorological Department (KMD) is forecasting a strong likelihood of El Niño. KMD put the chance of a severe El Niño at 81% and said there is a 97% probability that wetter-than-normal conditions will persist into the first months of 2027. Officials expect the October–December rains to be amplified by a combination of El Niño and higher Indian Ocean temperatures.
# Why health officials are alarmed Health has treated the forecast as a public-health warning. The Secretary for Public Health, Mary Muthoni, wrote to all county governors instructing them to prepare for outbreaks and service disruptions associated with heavy rains and flooding.
The ministry listed illnesses that typically rise after major floods: cholera, other diarrhoeal diseases, malaria and Rift Valley Fever (RVF). RVF risk is concentrated near rivers and overflowing dams, with the ministry naming Marsabit, Wajir, Isiolo, Mandera and Garissa as counties at particular risk for RVF.
# Where the risk is highest Counties the ministry singled out for high flood risk include Mandera, Wajir, Marsabit, Garissa, Kitui, Makueni, Machakos, Lamu, Kilifi, Kwale, Tana River, Taita Taveta and Mombasa. Additional at-risk areas include Budalang'i, Kano and the Tana Delta.
# What past seasons show The ministry recalled the 2023–24 El Niño season to show what can happen: 175 deaths, 40 people missing, 242 injured, more than 384,000 people displaced into 170 temporary camps, and 64 health facilities damaged or rendered unable to provide services. Officials also referenced Kenya's worst recent El Niño, 1997–98, which caused roughly 2,000 deaths and affected more than 1.5 million people.
# What public-health leaders say Assistant Director of Forecasting Services David Koros described the meteorological drivers for the upcoming rains: El Niño combined with Indian Ocean warming. The Director of Public Health, Dr Stephen Muleshe, warned the main expected challenges are waterborne disease outbreaks, flood-related injuries and disruption of nutrition and health services.
Humanitarian organizations are reacting. The Kenyan Red Cross said it is mobilising resources and preparing for scenarios that could be worse than anything seen in the last 20 years.
# Practical implications for counties and responders
# Bottom line Meteorological and health authorities are issuing early warnings and specific county-level alerts because a strong El Niño and continued heavy rains are likely. The combination of meteorological forecast, recent El Niño impacts, and identified high-risk counties creates a narrow window for preparedness to reduce disease outbreaks and health-system disruption.