Mombasa is sitting on a climate time bomb, scientists have warned, one that could see parts of the coastal city disappear under the ocean unless urgent action is taken.
Rising sea levels, worsening heatwaves, eroding coastlines, and sinking land are converging to make Mombasa one of the most vulnerable cities in Africa to the effects of climate change.
Mombasa sits precariously just metres above sea level, making it one of Africa's most vulnerable urban centres to climate change. The city of 1.2 million people—which handles 95 per cent of Kenya's international trade—faces an unprecedented combination of threats that could reshape its coastline and displace hundreds of thousands of residents.
Speaking at the opening of the Second Lead Author Meeting of the Intergovernmental Panel on Climate Change (IPCC) in Mombasa this week, climate scientist Cromwell Lukorito painted a stark picture of the city's future.
"We are seeing entire communities in the northern coastal strip being pushed inland," said Lukorito, IPCC Vice Chair and researcher at the University of Nairobi. "If this trend continues, even major infrastructure like the Mombasa–Malindi road could end up submerged."
A Seawall at the front part of Fort Jesus in Mombasa County helps break the intensity of waves and its effects on the coastline.
Photo credit: Photo | Wachira Mwangi
The warning comes as nearly 100 climate experts from 56 countries gather in the very city they're studying to draft the IPCC's landmark report on climate change and cities—a document that will inform global climate policy when released in March 2027.
Global sea levels have risen approximately 23 centimetres since 1880, with the rate of increase accelerating to 3.6 millimetres per year since 2006, according to NASA data. But Mombasa faces additional challenges that amplify this threat:
Land Subsidence : Parts of the city are sinking at rates of up to 5 millimetres annually due to groundwater extraction and the weight of rapid urban development.
Extreme Weather : Climate models predict a 20-40% increase in extreme precipitation events for East Africa, overwhelming Mombasa's already inadequate drainage systems.
Population Pressure : The city's population has doubled since 2000, with much of the growth occurring in low-lying coastal areas that flood regularly.
The combination means some areas of Mombasa could experience relative sea level rise of up to 50 centimetres by 2050—enough to permanently flood neighbourhoods that are home to tens of thousands of people.
The crisis extends beyond flooding. In Tudor, one of Mombasa's oldest neighbourhoods, residents like Amina Juma have watched their wells turn brackish as saltwater intrudes into the freshwater aquifer.
"Five years ago, we could drink water from our well," says Juma, who runs a small restaurant. "Now it's so salty we can't even cook with it. We have to buy all our water, and business is suffering."
Saltwater intrusion affects agriculture across the coastal region, with farmers reporting crop failures up to 15 kilometres inland. The Kenya Agricultural and Livestock Research Organisation estimates that saltwater intrusion costs the coastal economy approximately $12 million annually in lost agricultural productivity.
Perhaps nowhere is the ecological crisis more visible than in Mombasa's mangrove forests. These critical ecosystems, which serve as natural barriers against storms and nurseries for fish, are being squeezed between rising seas and expanding urban development.
Fishing boats parked in filth-choked waters at a beach in Mlango wa Papa in Mombasa Old Town.
Photo credit: Mercy Chelangat | Nation Media Group
Satellite imagery shows that Mombasa has lost 35 percent of its mangrove cover since 1990, with the rate of loss accelerating in recent years. The remaining forests are retreating inland at an average rate of 2 meters annually—but urban development blocks their migration path.
"How far can mangroves retreat before they disappear? That is the question scientists must urgently address—not just for Kenya, but for all of Africa," warns Lukorito.
The loss has immediate economic consequences. Mangroves support fisheries that employ over 30,000 people in Mombasa County and provide an estimated $15 million annually in ecosystem services, including storm protection and carbon storage.
Despite the challenges, Mombasa is emerging as a testing ground for climate adaptation in African cities. Governor Abdulswamad Sheriff Nassir points to the city's Climate Action Plan (2023-2050) as a model for urban climate resilience.
"Mombasa stands both as a symbol of exposure to climate shocks and a hub for bold responses," Nassir said during the IPCC meeting. "We are no longer waiting for solutions from elsewhere—we are creating them ourselves."
But local efforts face a critical obstacle: funding. Kenya's major urban centres, including Mombasa and Nairobi, are excluded from the nationally financed climate action programs due to their classification as large cities.
"Our major urban centres are excluded from the national climate finance mechanism," acknowledges Dr Festus Ng'eno, Principal Secretary at the Ministry of Environment, Climate Change and Forestry. "This is a challenge, especially since these cities face the greatest risks—pollution, water stress, and heat."
International climate finance has been slow to reach African cities. Of the $100 billion annually pledged by developed countries in 2009 for climate action in developing nations, less than 10 percent reaches urban adaptation projects, according to the Climate Policy Initiative.
The IPCC meeting in Mombasa represents a critical moment for climate science and policy. For the first time, an IPCC special report will focus exclusively on cities, which house more than half of the world's population and generate 70 percent of global greenhouse gas emissions.
"We are in a city that lives with the realities we are writing about—sea level rise, infrastructure pressure, and cultural vulnerability," explains Bart van den Hurk, Co-Chair of IPCC Working Group II. "That makes this meeting both urgent and deeply symbolic."
The report will include 13 African experts among its authors, ensuring that African perspectives shape global climate policy. It will also consider intangible losses, such as cultural heritage and tourism potential, as part of the climate risk equation. Mombasa’s historic Old Town and Fort Jesus are among the sites at risk of deterioration due to flooding and saltwater intrusion.
“This report will help us shape policies that are grounded in scientific realities. While most environmental programmes are devolved, our role is to issue policy direction. Cities like Mombasa are key in delivering climate resilience, especially through the blue economy,” said PS Ng’eno.
The IPCC report will undergo rigorous peer review over the next two years before its March 2027 release.
“As President Ruto said at COP27, Africa has what it takes to lead global climate solutions, land, renewable energy, and a youthful population. But to do that, we need the right science and policy tools to protect our people,” he said.
The week-long IPCC meeting will conclude with a Pan-African outreach session to enhance regional cooperation on cities and climate change.
