Kenya Maps 18 High-Risk Areas Ahead of Expected El Niño Rains From October

Kenya has stepped up preparations for a potentially strong El Niño event expected to influence weather conditions from October 2026, with the government identifying 18 high-risk counties and urban areas that could face flooding, landslides, disease outbreaks, drought and infrastructure damage.

Interior Cabinet Secretary Kipchumba Murkomen said the government had completed a risk assessment to help authorities prepare for the expected October-November-December (OND) rainfall season.

The assessment comes as weather forecasts point to above-normal rainfall in several parts of Kenya during the final quarter of the year. Kenya Meteorological Department forecasts have placed the probability of a very strong El Niño at 81%, while there is a 97% probability that its influence could continue into early 2027.

Areas placed under closer watch

The government’s assessment covers different regions, with the risks varying depending on local geography and existing vulnerabilities.

In the Coast region, the counties identified are:

• Tana River
• Kilifi
• Lamu
• Mombasa
• Kwale

These areas could experience flooding, storm surges, coastal erosion and damage to infrastructure. Communities living in low-lying areas may be particularly vulnerable if heavy rainfall overwhelms drainage systems and rivers.

The Lake Basin has also been placed under close monitoring. The counties named are:

• Kisumu
• Busia
• Siaya
• Homa Bay
• Migori

The government has identified possible flooding, landslides, disease outbreaks and displacement among the major risks in this region.

In the Rift Valley, the assessment highlights:

• Turkana
• Baringo
• West Pokot
• Narok

Unlike the Coast and Lake Basin, the risks in these counties are more varied. Authorities are preparing for possible flash floods and landslides in some areas, while drought, livestock losses and food insecurity could affect vulnerable communities elsewhere.

The North Eastern region is represented by:

• Garissa
• Wajir
• Mandera

The main concerns include water shortages, poor pasture, livestock losses, drought and food insecurity.

Nairobi also among areas requiring special preparedness

Nairobi has been identified as a high-risk urban centre alongside Mombasa and Kisumu.

The major concern for the capital is flooding caused by intense rainfall, particularly where drainage systems become overwhelmed. Heavy rains can also disrupt transport, damage infrastructure and interfere with essential services.

Mombasa and Kisumu are similarly vulnerable because of their locations and existing exposure to flooding.

This means the government’s broader assessment covers 18 areas when Nairobi is counted alongside the 17 counties specifically listed by region. Mombasa and Kisumu are already included in the regional county lists but are separately highlighted because of their urban risks.

Why the October rains are attracting attention

The warning is linked to the anticipated development of El Niño during the OND season.

Kenya’s Meteorological Department has previously explained that El Niño is an important climate driver but does not, by itself, determine exactly how much rain Kenya will receive. The Indian Ocean Dipole (IOD) is another major factor influencing rainfall over East Africa.

The latest forecast indicates that above-average rainfall could become more widespread from October, with October and November expected to carry the strongest wet signal.

KMD has also cautioned that a strong El Niño does not automatically mean that every part of Kenya will receive destructive rainfall. The intensity and distribution of rainfall will depend on several interacting climate factors.

Government activates emergency teams

The government says the risk mapping is intended to move disaster management from reaction to preparedness.

According to Murkomen, national emergency, multi-agency and county response teams have been placed on high alert and are being sensitised about their responsibilities ahead of the expected weather conditions.

The National Disaster Operations Centre has been involved in identifying areas vulnerable to different hazards. The information is expected to help authorities determine where emergency resources and response teams may be required most urgently.

The government has also indicated that the list is not necessarily final. Additional areas could be included if subsequent assessments establish that they face significant risks from the anticipated weather pattern.

Flooding is not the only concern

Although El Niño is commonly associated with heavy rainfall and flooding in Kenya, the government’s assessment highlights a more complicated picture.

Some counties may experience excessive rainfall and flooding, while others could simultaneously face drought-related challenges.

For example, parts of the North Eastern region remain vulnerable to water shortages, poor pasture and livestock losses. In parts of the Rift Valley, authorities are preparing for a combination of drought, flash floods and landslides.

This variation is important because the impact of El Niño is unlikely to be uniform across the country. Local geography, drainage infrastructure, river systems, soil conditions and existing environmental conditions can determine how communities experience the same weather event.

Farmers and livestock keepers face an uncertain season

The anticipated rainfall could provide important benefits to agriculture if it is well distributed.

Adequate rainfall can replenish water sources, improve pasture and support crop production, particularly in areas that have experienced moisture deficits.

However, excessive or poorly distributed rainfall could create new problems. Farmers may face soil erosion, crop damage, waterlogging and disease outbreaks, while livestock keepers could experience animal losses where floods destroy grazing areas or cut off access to water and markets.

For this reason, the government’s early warning approach is particularly important for communities whose livelihoods depend heavily on weather conditions.

Health risks could also increase

Heavy rainfall and flooding can create conditions favourable for the spread of some waterborne and vector-borne diseases.

Flooding can contaminate water sources, disrupt sanitation systems and force families to move from their homes. Standing water can also create breeding environments for mosquitoes.

The government has therefore included disease outbreaks among the risks being monitored as part of the national El Niño preparedness plan.

Health facilities in vulnerable counties may also need to prepare for increased demand if flooding causes injuries, displacement or outbreaks of infectious diseases.

Transport and infrastructure could come under pressure

Another major concern is the potential impact on roads, bridges, drainage systems and other public infrastructure.

Heavy rainfall can quickly damage roads, trigger landslides and make some routes impassable. In urban areas, blocked drainage channels can turn roads and residential areas into flood zones within a short period.

For Nairobi, Mombasa and Kisumu, the risk is particularly significant because large populations and economic activities depend on transport and other essential services operating normally.

Early intervention on drainage systems, bridges and vulnerable roads could therefore help reduce the cost of emergency repairs once the rains begin.

Kenya is preparing before the rains arrive

The latest warning is significant because authorities are beginning preparations well before the anticipated October onset.

Kenya Meteorological Department’s seasonal forecasting system is designed to provide rainfall and temperature outlooks that can support planning across sectors including agriculture, health, water, energy, transport and disaster management.

For residents in the identified areas, the latest government warning is a reminder to pay attention to official weather alerts rather than waiting until extreme weather has already begun.

Households in flood-prone locations can use the time before October to identify safer routes, protect important documents, clear drainage around homes and establish emergency communication plans.

The bigger picture

Kenya’s preparations come amid wider international concern over the developing El Niño event.

The World Meteorological Organization has warned that the event is strengthening, with the possibility of a strong El Niño between August and October and wetter-than-normal conditions expected in parts of the Greater Horn of Africa.

The situation therefore extends beyond Kenya’s borders, with other countries in the region also monitoring possible effects on agriculture, water supplies, food security and disaster risks.

For Kenya, the government’s decision to map vulnerable areas before the October rains provides an opportunity for national and county authorities to strengthen preparedness while there is still time to act.

The key challenge will now be turning the risk assessment into practical measures on the ground.

With the possibility of above-normal rainfall approaching, early warnings, functioning drainage systems, emergency response teams and informed communities could make the difference between a manageable rainy season and a major disaster.