The Port of Mombasa is Kenya’s only international seaport and the biggest port in East Africa, built around Kilindini Harbour, a natural deep-water inlet on the south-west side of Mombasa Island on the Indian Ocean. According to the Kenya Ports Authority, it handled 45.45 million tonnes of cargo and 2.11 million TEU of containers in 2025, up from 2 million TEU in 2024. The modern harbour dates from 1896, when work began at Kilindini on the Uganda Railway. It matters well beyond Kenya: its hinterland reaches Uganda and the other landlocked states of the Great Lakes, and transit cargo for those neighbours made up 15.88 million tonnes of the 2025 total.
A port is a machine for moving cargo between ship and land, and Mombasa’s machine has an unusual layout: a coral island, two creeks, a deep drowned valley, and a railway running inland for hundreds of kilometres. This article takes the parts in order, from the water to the rails, and then looks at what they add up to for Kenya and its neighbours.
Kilindini: A Drowned River Valley up to 55 Metres Deep
Mombasa Island is a coral outcrop about 5 km long and 3 km wide, cut off from the mainland by two tidal creeks. To the north is Tudor Creek and the old harbour of Port Tudor, guarded since the 1590s by the Portuguese Fort Jesus, a UNESCO World Heritage Site since 2011. To the south and west lie Kilindini Harbour and Port Reitz, the deep water that carries the modern port. Mombasa, Kenya’s second city, had about 1.21 million people in the 2019 census, and many port workers live in mainland townships such as Mikindani, whose working-class estates house people employed in the Changamwe industries and at Kilindini.
For most of Mombasa’s history the old harbour on the Tudor side did the work. Vasco da Gama called in 1498, the first known European visitor, and the 16th-century Portuguese writer Duarte Barbosa described a harbour busy with small craft and great ships from Sofala, Cambay and Malindi. The town exported ivory, millet, sesame and coconuts across the Indian Ocean to Arabia, Persia, India and China. Mombasa was also the first capital of British East Africa until Nairobi took over in 1907.
Kilindini is a ria, a river valley that the sea flooded when sea levels rose, and that geology is the port’s great advantage. The inlet is 25 to 30 fathoms, or about 46 to 55 metres, deep at its centre. The name comes from Swahili and means “deep down” or “in the depths”. Depth inside the harbour is not the limit; the controlling depth is the outer channel through the approaches, which has been dredged to 17.5 metres.
The 1942 Fleet Anchorage and Its Code-Breakers
The same deep, sheltered water made Kilindini a naval anchorage. From early 1942, while Kenya was a British colony, it served as the temporary base of the British Eastern Fleet until the Japanese threat to Colombo in Ceylon had passed. Nearby, the Far East Combined Bureau, an outstation of the code-breakers at Bletchley Park, worked from the requisitioned Allidina Visram High School in Mombasa and succeeded in breaking Japanese naval codes.
Kenya Ports Authority and the Berth 19 Expansion
The harbour is run by the Kenya Ports Authority, a state corporation created by an act of parliament in 1978, whose headquarters sit inside the port. The authority also manages Kenya’s smaller seaports, including Lamu, Malindi, Kilifi, Mtwapa, Kiunga, Shimoni, Funzi and Vanga, and has offices at the inland dry ports of Nairobi, Naivasha and Eldoret and at Kisumu on Lake Victoria. In 1989 the government also placed the island’s ferries, including the Likoni service, under a KPA subsidiary, Kenya Ferry Services, which became an independent state corporation in 1998.
The quays at Kilindini have been extended in stages. The most recent documented step was launched in July 2011: a US$82.15 million project by the Kenyan government, built by China Road and Bridge Corporation, that let the port handle Panamax ships from 29 August 2013. It added a new berth, Berth 19, with 6.1 hectares of stacking yard and about 200,000 TEU of extra annual capacity, and was intended to raise the port’s throughput by about a third.
Crossing the Water: Likoni Ferry, Makupa Causeway and Nyali Bridge
Because the port surrounds an island, moving people and goods across the creeks is part of how it works. Three routes carry traffic off the island. To the north-west, the Makupa Causeway, built by the colonial government in 1929 to replace the 1899 Britannia Bridge, carries both the main A109 road to Nairobi and the old metre-gauge railway between Tudor Creek on the east and Port Reitz Creek on the west. To the north-east, the Nyali Bridge, a 391.65-metre concrete box-girder bridge completed in 1980, crosses Tudor Creek. A separate road and rail bridge serves the mainland container area near Port Reitz.
To the south there is no bridge at all. The Likoni Ferry, running since 1937, crosses Kilindini Harbour, a distance of about 500 metres, between the island and the mainland suburb of Likoni. Seven double-ended ferries share the water with the ships heading for the berths; foot passengers and cyclists ride free, while vehicles pay a toll, from KSh 50 for a motorcycle to KSh 1,100 for a bus. The crossing has a grim safety record: on 29 April 1994 the ferry Mtongwe capsized 40 metres from shore, killing 272 of the 400 people aboard. A bridge or tunnel from Likoni to the island has been proposed, but the cost has made both unlikely. To ease the pressure, the Dongo Kundu bypass, completed in July 2024, links the South Coast with the Nairobi highway at Miritini without passing through the island.
From the 1896 Uganda Railway to the Madaraka Express
The port exists in its present form because of a railway. The metre-gauge Uganda Railway was begun at Mombasa in 1896 and reached Kisumu on Lake Victoria in 1901, 1,060 km inland. Its rails, 1.2 million sleepers, fish-plates, bolts and steel girders all had to be imported from India, and landing that material required a modern port at Kilindini. Nairobi itself was founded as a depot on the line.
By the 2000s the colonial line was worn out: freight carried from the port by rail fell from 4.8 million tonnes a year in the 1980s to 1.5 million tonnes in 2012, and the last metre-gauge train between Mombasa and Nairobi ran on 28 April 2017. Its replacement is the Mombasa–Nairobi Standard Gauge Railway, completed in 2017 at a cost of US$3.6 billion. China Road and Bridge Corporation was the prime contractor and hired about 25,000 Kenyans to build it. Freight trains run from Port Reitz, just west of the island, to the inland container depot at Embakasi in Nairobi; commercial freight began on 1 January 2018, and by November 2018 the line was running 30 freight trains a day, including double-stacked container trains. An extension of 120 km to Naivasha and Suswa was completed in October 2019, taking Kenya’s standard-gauge network to about 592 km. Passenger trains, branded the Madaraka Express, began on 1 June 2017 between the Mombasa Terminus at Miritini and Nairobi. As of 2020 the railway’s operating costs exceeded its revenue.
45.45 Million Tonnes in 2025: Where the Cargo Goes
The Kenya Ports Authority’s 2025 figures show the machine running harder. Total cargo rose by 10.9%, or 4.46 million tonnes, to 45.45 million tonnes. Container traffic grew 5.5% to 2.11 million TEU. The fastest-growing part was transit cargo for landlocked neighbours, above all Uganda, which rose 19.5% to 15.88 million tonnes, roughly a third of everything the port handled.
That transit share is why the port’s efficiency matters in Kampala and beyond as much as in Nairobi. A container landed at Kilindini can leave by standard-gauge train for Nairobi and Naivasha, or by lorry along the highway west, and every hour saved at the quay shortens the trip to a country with no coast of its own. The East African Railway Master Plan provides for linking Kenya’s standard-gauge line with new lines in neighbouring countries, which would extend the port’s reach further.
Dongo Kundu: A 1,200-Hectare Free Port
Kenya’s plans for the next stage lie on both sides of Mombasa. At Dongo Kundu, on the mainland near Mombasa, the government is developing a free port on 1,200 hectares of Kenya Ports Authority land through public–private partnerships, served by the new bypass road.
Lamu Port and the LAPSSET Corridor
Further north, a new international port is being built at Lamu as part of the US$24 billion Lamu Port–South Sudan–Ethiopia Transport (LAPSSET) corridor. Plans call for 32 berths eventually and an entrance channel dredged to 18 metres, deep enough for Post-Panamax ships of 120,000 deadweight tonnes, deeper than Mombasa’s 17.5-metre approach. In August 2014 the ports authority signed a US$478 million contract with China Communications Construction Company for three berths. Although Lamu is planned to be larger than Kilindini, the Kenya Ports Authority says the two ports will complement rather than compete with each other.
From the drowned valley at Kilindini to the double-stack trains leaving Port Reitz, each piece of Mombasa’s system was built to push cargo inland. For the landscape that railway crosses, from the coast to the Rift Valley, see our guide to Kenya’s geography. The countries that rely on the port for sea access are listed in our guide to landlocked countries, and the city at the other end of the line is profiled in Nairobi, capital of Kenya.