By the NGOs.ke Editorial Team. Updated 27 October 2026.
Kenyan NGOs should treat the 2026 short rains as a health and food-security emergency in waiting, not only a flood event. The Kenya Meteorological Department puts the chance of above-normal October to December rainfall at 99 per cent, the World Meteorological Organization now says this El Niño could reach unprecedented strength, and the Ministry of Health has issued an advisory to all 47 counties covering cholera, typhoid, malaria, dengue, Rift Valley fever and child malnutrition. This guide turns those warnings into a practical checklist for organisations working in the highest-risk counties.
What is the El Niño forecast for Kenya in late 2026?
On 23 October 2026 the WMO warned that sea surface temperatures in the tropical Pacific could reach 3.8°C above average between November 2026 and January 2027. Its Secretary-General, Celeste Saulo, said conditions were “literally off the monitoring charts that we have used for the past four decades”. The monthly Niño 3.4 index rose from 2.0°C to 2.8°C above average between July and September.
For Kenya, the Met Department expects above-average short rains across much of the country, with onset and distribution varying by region. Kenya Met deputy director Kennedy Thiong’o has advised farmers to rely on county-specific forecasts from county meteorological offices rather than the national outlook. A very strong event can also bring drought to some regions while flooding others, which is why the same county can face both problems within a season.
Which counties are most at risk?
Two government lists exist and they overlap. The Interior Ministry flagged 18 counties in August for floods, disease outbreaks, food shortages and displacement. The Health Ministry’s later advisory names the areas where health systems are most exposed.
| Source | Counties and areas named |
|---|---|
| Interior Ministry (August 2026) | Nairobi; Tana River, Kilifi, Lamu, Mombasa, Kwale; Kisumu, Busia, Siaya, Homa Bay, Migori; Turkana, Baringo, West Pokot, Narok; Garissa, Wajir, Mandera |
| Health Ministry advisory (all 47 counties) | Mandera, Wajir, Marsabit, Garissa; Kitui, Makueni, Machakos; Lamu, Kilifi, Kwale, Tana River, Taita Taveta, Mombasa; Kano Plains, Budalang’i, Tana Delta, Gusii Highlands, West Pokot and Rift Valley escarpment landslide zones |
If your programme sits in any county on either list, assume it will be affected and plan accordingly.
Why does Rift Valley fever matter for NGOs?
The regional climate centre ICPAC has warned that El Niño can create conditions favourable to Rift Valley fever across East Africa and named Kenya among the most exposed countries. It said that without coordinated early warning and response, outbreaks could devastate herds and disrupt trade. The Health Ministry lists the disease alongside cholera and malaria in its advisory.
The practical consequence is that livelihoods programmes in pastoral counties, not only health programmes, need an outbreak plan: who talks to county veterinary officers, how community members are told to handle sick animals, and what happens to cash and food support if livestock markets close.
What did the last El Niño cost, and what does it tell us?
Government figures for the 2023-2024 El Niño rains give a baseline for planning:
- 43 counties were affected.
- 175 people died, 40 went missing and 242 were injured.
- 384,216 people were displaced into 170 camps.
- 64 of 1,434 health facilities assessed in 11 counties became inaccessible.
The facility figure is the one most often missed in NGO plans. Roads and clinics, not only homes, go under water. If your organisation depends on a single access road or a single partner clinic, that is your first risk to fix.
Where does the existing hunger crisis fit in?
The rains arrive on top of a food-assistance system that was already stretched. FEWS NET’s June 2026 outlook estimated that 3.0 to 3.49 million people would need humanitarian food assistance between June and January, peaking in September and October. In the Dadaab, Kakuma and Kalobeyei refugee settlements it projected Crisis (IPC Phase 3) outcomes through January, with a risk of Emergency (Phase 4) if WFP funding stopped after September, since funding was then confirmed only through that month. It also expected Mandera to stay in Phase 3 through January even as other pastoral areas improved. Check current WFP and county figures before you finalise any caseload, because these projections date from June.
FEWS NET also noted that floods displaced about 136,000 people in 2023. Different agencies count different periods, so cite the source and date whenever you quote a displacement number.
What should NGOs do before the rains peak?
- Map your sites against both county lists. Mark which offices, stores, clinics and water points flood, and which roads you lose first.
- Pre-position stock now. The government is moving medicines, nutrition supplies, cholera response materials and mosquito-control products to likely need areas. Agree with the county health team what you will hold so supplies are not duplicated in one place and missing in another.
- Plug into coordination. The National Public Health Emergency Operations Centre, the National Disaster Operations Centre and county governments lead, with WHO, UNICEF, WFP and Kenya Red Cross as supporting partners. Ask your county steering group how to be listed.
- Test water, then chlorinate. Counties have been asked to test drinking water safety. Our cholera prevention and WASH guide for NGOs sets out the household and community measures.
- Protect children’s nutrition. Keep screening and treatment running if roads close, and plan for community health workers to reach children when facilities cannot be reached.
- Budget for psychosocial support. The Health Ministry asked counties to provide mental health and psychosocial support throughout the period, which is a gap NGOs commonly fill.
- Write down triggers for action. Our anticipatory action guide explains how to tie funding to a forecast so money moves before the flood, and our short rains flood response guide covers how to give and respond responsibly once it hits.
Frequently asked questions
How likely are above-normal short rains in Kenya in 2026?
The Kenya Meteorological Department puts the chance of above-normal rainfall for October to December at 99 per cent, according to the Health Ministry’s briefing. Rains may continue into February 2027.
Is El Niño 2026 expected to be stronger than 2023?
The WMO says this event could reach unprecedented strength, with Pacific temperatures projected up to 3.8°C above average between November 2026 and January 2027. Local impacts depend on region, so use county forecasts.
Which diseases are most likely to rise during the rains?
The Health Ministry advisory flags cholera, typhoid, malaria, dengue fever and Rift Valley fever, plus drowning and flood injuries and malnutrition among children if food supplies are disrupted.
Can NGOs help before the floods arrive?
Yes. Pre-positioning supplies, mapping access routes, training community volunteers and agreeing response roles with county teams all cost far less before the rains than during them.
Where can I follow the forecast?
Use your county meteorological office for local outlooks, and the World Meteorological Organization for global El Niño updates.
Figures come from the WMO (via The Star, 23 October 2026), the Interior Ministry notice reported on 10 August 2026, the Health Ministry briefing reported by KBC, and FEWS NET’s June 2026 Kenya outlook. Check official sources for the latest advisories before acting.
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