When floods strike, public attention naturally turns to submerged roads, damaged homes and displaced families.
Yet another emergency can develop beyond immediate public view: drinking-water sources become contaminated, sanitation systems fail, health facilities become difficult to reach, and communities face growing exposure to disease. If these risks are not addressed early, a weather emergency can quickly become a public health crisis.
This is the threat Kenya must prevent as the country prepares for El Niño rains. Floodwater can carry sewage and other contaminants into rivers, wells and household water supplies, increasing the risk of cholera, typhoid, dysentery, hepatitis A and other diarrhoeal diseases. Stagnant water can also create breeding sites for mosquitoes, while damaged roads and disrupted supply routes may delay emergency referrals, interrupt the delivery of medicines and leave vulnerable patients without essential care. These consequences must never be accepted as inevitable.
The most important work begins before outbreaks occur and before communities become isolated. Disease surveillance must detect unusual patterns of illness early. Laboratories must be ready to confirm suspected cases quickly. Medicines, diagnostic supplies and emergency commodities must be positioned where they can still be reached when normal supply routes are disrupted. Health facilities must also have practical contingency arrangements to remain operational.
This is the purpose of the Health Sector El Niño Contingency Plan. It is not simply a document for use after disaster strikes; it is a framework for anticipating health risks, protecting essential services and acting before threats escalate.
The Ministry of Health is working with county governments, emergency agencies, humanitarian organisations and development partners through established coordination and emergency-response structures. The priority now is to ensure that national preparedness translates into practical readiness in counties, health facilities and communities.
Early detection is central to that readiness. During flooding, the difference between a contained health threat and a widespread outbreak can be a matter of days. Health teams need functioning routine and event-based surveillance, rapid-response capacity, and reliable information from affected communities. When an alert is raised, laboratory and sample-referral systems must provide timely confirmation so that the appropriate response can begin without delay.
Preparedness must extend equally to the health supply chain. Flooded or damaged roads can cut off communities precisely when medicines, emergency health kits, laboratory materials, nutrition commodities and infection-prevention supplies are most needed. Pre-positioning these commodities, together with alternative arrangements for reaching inaccessible areas, can prevent dangerous interruptions in essential services.
Safe water and sanitation are just as critical. Preventing contaminated water from causing illness requires more than issuing warnings. Water-quality surveillance must be accompanied, where necessary, by chlorination, household water treatment, disinfection of contaminated sources, temporary sanitation facilities and accessible handwashing points. Clear, practical information must reach households early enough for them to act.
At the same time, the health system cannot focus only on illnesses directly associated with flooding. A woman in labour will still require skilled care. A child with severe diarrhoea or acute malnutrition will still need urgent treatment. People living with HIV, tuberculosis, diabetes, hypertension and other chronic conditions will continue to depend on medicines and clinical follow-up. Patients requiring emergency care cannot simply wait for roads to reopen.
Keeping health facilities functional, maintaining referral and evacuation arrangements, providing backup power and safe water where necessary, and deploying temporary clinics or mobile outreach services can therefore be as important as controlling an outbreak. Continuity of essential healthcare must remain at the heart of the emergency response, with particular attention to children, pregnant women, older persons, persons with disabilities and communities that are difficult to reach.
Communities themselves will determine much of what happens next. Community Health Promoters and Primary Care Networks provide a vital connection between households and the health system. They can help families recognise danger signs, promote safe water and food practices, communicate early warnings, counter misinformation and link people who need treatment to appropriate services.
Protecting public health during floods, however, cannot rest on health workers alone. Every household has a role. Families should ensure that drinking water is safe and stored in clean, covered containers. Food should be thoroughly cooked and protected from contamination. Handwashing with soap and safe water remains one of the simplest and most effective protections against infection.
Anyone who develops persistent fever, severe diarrhoea, repeated vomiting, blood in the stool or signs of dehydration should seek care promptly. Delaying treatment or self-medicating with antibiotics can worsen illness and contribute to antimicrobial resistance.
Communities must also follow evacuation and safety instructions. Attempting to walk or drive through floodwater can turn an already dangerous situation into a tragedy. Misinformation can likewise undermine emergency operations and delay people from seeking appropriate care. Public communication must therefore be timely, consistent, trusted and practical.
Effective preparedness requires national and county governments to work in concert, health facilities to maintain readiness, partners to align their support with identified needs, and communities to receive reliable information early enough to act. It also requires accountability: plans must be tested, gaps addressed and resources directed to the areas of greatest risk.
The success of preparedness will not be measured by the number of plans developed or coordination meetings held. It will be seen in contaminated water sources made safe, outbreaks detected before they spread, medicines reaching isolated communities, health facilities remaining operational and patients continuing to receive care when they need it.
We cannot control how much rain falls. But we can determine whether heavy rainfall is allowed to become a wider health emergency. The time to protect public health is not after the floods arrive. It is now.
Article by Mary Muthoni, Principal Secretary for Public Health and Professional Standards.
Views expressed in this article do not in any way represent the position of Kenya Broadcasting Corporation.
