The Mombasa County Government is fixing its drainage system to prevent flooding as the coastal city braces for severe El Niño-induced short rains.
Consequently, in the wake of the looming threat of extreme El Niño climate variability, the coastal county has launched a multi-site drainage clearing exercise to curb flooding in Mombasa and its environs.
Maintenance teams are actively unclogging major storm drains, clearing waste, and finishing box culverts in collaboration with national agencies.
El Niño is a natural climate phenomenon which occurs every two to seven years when sea surface temperatures rise in the tropical eastern Pacific, affecting weather globally.
The Kenya Meteorological Service Authority has forecast above-average rainfall across more than 80 per cent of the country for the October–December 2026 short rains season, driven by intensifying El Niño conditions.
Governor Abdulswamad Nassir has directed the department of environment, water and solid waste management to ensure that the drainage systems in the six sub-counties of Mvita, Nyali, Likoni, Changamwe, Jomvu and Kisauni are thoroughly cleared of debris.
Nassir said the devolved government is also constructing new stormwater drainage systems to improve water flow, reduce flooding and protect homes, businesses and road users during heavy downpours.
The governor said his administration has done verification of flood hotspots across all the 30 administrative wards in the six sub-counties and cleared drainage channels using heavy-duty equipment like hydro-jetters.
“We want clean drainage systems in the sub-counties to avoid flooding,” he said, adding that the county is strengthening its El Niño preparedness across Mombasa.
Nassir says his administration has already identified several flooding hotspots, fixing the infrastructure and protecting people before the rains intensify.
“The public must remain alert, heed official weather advisories and avoid unnecessary exposure to identified high-risk areas,” he said, adding that ‘preparedness is our strongest defence’.
He went on, ‘multi-agency teams are mapping vulnerable areas, clearing critical drainage channels and pre-positioning emergency, health, rescue and humanitarian resources to mitigate the anticipated challenges and safeguard lives, livelihoods and property.’
A recent report by the National Disaster Operations Centre (NDOC) has identified Nairobi, Mombasa and Kisumu as among the high-risk urban hotspots even as it predicted that the ongoing El Niño is set to peak in December.
According to the NDOC, residents of Nairobi, Mombasa and Kisumu are at great risk of flooding, drainage blockages, strain on infrastructure and disruption to essential public services, including transport, healthcare, water supply and power networks.
Nassir said Mombasa has been flagged as a high-risk urban hotspot for severe flooding, storm surges and infrastructure damage in the event of heavy El Niño rains.
Nassir has disclosed that 300 officers drawn from the county government and national agencies have already participated in rescue, marine safety, casualty management and emergency-response exercises.
Mombasa is among the high-risk urban centres flagged by the national government to experience heavy, above-average rainfall and potential flooding from the intensifying 2026 El Niño.
Scientists contend that El Niño, as part of a larger climate cycle, is a naturally occurring climate phenomenon characterised by the abnormal warming of the Pacific sea surface temperatures.
The World Meteorological Association (WMA) warns that the El Niño climate phenomenon could bring droughts, flooding, heat waves and displacement of people around the world later this year.
According to WMA, October to December 2026 is a critical rainfall period for Kenya and other countries in the region.
The international weather agency warned that the anticipated heavy rainfall could have far-reaching consequences across many sectors, including transportation, agriculture, health and infrastructure.
The national government has activated an Ad Hoc Cabinet Committee on El Nino preparedness that will also support the devolved governments.
Nassir says the devolved government remains alert and proactive and is putting in place coordinated action to minimize the impact of heavy rains.
“This will be no ordinary rainy season, and our response cannot be ordinary. Mombasa is preparing early, mobilizing every available resource and working across agencies to protect lives, livelihoods and property,” he said.
The coastal county boss says a multi-agency team is in place to coordinate the port city’s preparedness and emergency response.
“We are fully prepared to respond to potential El Niño-linked disasters such as flooding, storm surges, coastal erosion along the shoreline and infrastructure damage,” he said.
Nassir said in the 2023 El Niño rains, nearly 3,900 households were affected, underscoring the need to move from reacting to disasters to anticipating and preventing them.
“We have therefore developed a comprehensive multi-agency contingency framework anchored on early warning, early action, coordinated response and rapid recovery,” he said.
According to the Kenya Red Cross Society, the 2023 El Niño displaced 500,000 people across 43 counties and warns that this season’s severity index is projected to be even higher.
Mombasa County Commissioner Mohamed Noor said the authorities are putting in place a coordinated action from all the relevant stakeholders to respond to El Niño-linked disasters.
“The aim is to coordinate the actions of the national government, county government and humanitarian agencies to enable the rapid mobilisation of emergency resources,” he said.
Noor said chiefs and their assistants will be disseminating climate information down to the community level.
He said low-lying areas and informal settlements face heavy flood risks from above-average rainfall and remain a cause of major concern for the authorities.
The Kenya Maritime Authority (KMA) has also warned that rough sea conditions are very likely to prevail along the coastal strip between October and December 2026.
According to KMA, the conditions include strong winds, rough seas, high waves, heavy rainfall and reduced visibility, which pose a risk to vessels and persons undertaking activities at sea and along the coastline.
The KMA warning carries significant implications for fisherfolk, boat operators, and anyone with activities planned on or near the ocean.
On September 12, 2026, a tragic boating accident occurred in Mombasa when a leisure vessel named MV Blue Pineapple capsized due to heavy waves along Tudor Creek, resulting in the drowning of two people.
The public are advised to avoid venturing into the sea during periods of adverse weather and rough sea conditions.
KMA Director-General (DG) Omae Nyarandi has advised fishermen in the coastal counties of Mombasa, Kwale, Kilifi and Lamu to be cautious while venturing into the sea.
There is a possibility of surging waves during the high tide times in the low-lying areas of the coasts during the September-December period.
The Kenya Coast Guard Service (KCGS) has stepped up preparedness for potential flooding and other weather-related emergencies ahead of the anticipated El Niño rains.
KCGS said it is strengthening its operational readiness along the coastline amid the risk of heavy rainfall, rising water levels, strong currents, flash floods and rough sea conditions.
By Hussein Abdullahi
