Why cholera and malaria rise after floods, as Kenya expects above-average short rains

Why do cholera and malaria cases rise after floods? Floods can contaminate drinking water, which can spread cholera. They also leave standing pools where malaria mosquitoes can breed, which can raise malaria transmission some weeks later, according to the World Health Organization (WHO). The Kenya Meteorological Department (KMD) forecasts above-average rain in most counties during the October–December short rains.

KMD issued the outlook on 31 August 2026. It names 43 of Kenya's 47 counties for above-average rain, including Nairobi, Kisumu, Mombasa, Garissa and Kiambu, plus much of West Pokot, Samburu and Marsabit. Turkana is forecast near-average to above-average.

Cholera spreads when people swallow food or water contaminated with the bacterium Vibrio cholerae. WHO says symptoms appear 12 hours to five days after infection, and an infected person can pass the bacteria in faeces for one to 10 days. It ties the disease to limited access to safe water, basic sanitation and poor hygiene, and names floods among the climate events that can cause such gaps.

WHO's flood guidance, dated 29 January 2020, lists the contamination of drinking-water facilities among the most common flood risks and says standing water can be a breeding site for mosquitoes.

Malaria is a vector-borne disease, meaning one passed on by a living carrier such as a mosquito. It spreads mostly through the bites of infected female Anopheles mosquitoes, WHO says. Symptoms usually start within 10 to 15 days of a bite, and the most common early ones are fever, headache and chills. A 2006 WHO review explains the link to flooding: the first surge may wash away existing breeding sites, but standing water left by heavy rain or overflowing rivers can create new ones, and the mosquito population can grow “with typically some weeks delay”.

The same WHO review, Communicable diseases following natural disasters, records a cholera epidemic of more than 16,000 cases in West Bengal in 1998 that was attributed to preceding floods. After flooding in Bangladesh in 2004, a diarrhoeal outbreak of more than 17,000 cases was recorded, with Vibrio cholerae isolated. For malaria, the review says periodic flooding linked to the El Niño-Southern Oscillation has been associated with epidemics in the dry coastal region of northern Peru.

The review also says the overall risk of outbreaks after disasters is lower than often perceived and depends on the size, health and living conditions of displaced people. For mosquito-borne disease, the effect depends on the local mosquito species and its preferred habitat.

In Kenya, WHO's Africa office reported in its Week 39 situation report (21–27 September 2026) one confirmed cholera case in Nairobi County, with no new case in the past week.

On malaria, WHO estimates 282 million cases and 610,000 deaths worldwide in 2024, in 80 countries; the WHO African Region had 95% of cases (265 million) and 95% of deaths (579,000). The Kenya News Agency reported in April 2022 that Kenya's overall malaria prevalence was 6%, unevenly spread, with the highest burden in the lake endemic counties around Lake Victoria, where one in five people had malaria at any given time. Kisumu, Siaya and Busia are on KMD's above-average rain list.

The Ministry of Health's advice for the March–May long rains, in a statement signed by Public Health Principal Secretary Mary Muthoni Muriuki and reported by The Star on 8 March 2026, was to boil, chlorinate or otherwise treat drinking water by approved methods, wash hands regularly with soap, drain stagnant water around homes, sleep under insecticide-treated nets, not walk or drive through flooded areas, and go to the nearest health facility immediately for severe diarrhoea, vomiting, fever or difficulty breathing. WHO calls uninterrupted provision of safe drinking water “the most important preventive measure” after floods, and advises mosquito nets when sleeping where malaria is present.