"Kilindini" is an old Swahili term that means "deep".

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Kilindini Harbour is a large, natural deep-water inlet extending inland from Mombasa, which serves as the harbour for Mombasa, with a hinterland extending to Uganda. It is 25-30 fathoms (45–55 meters) at its deepest centre. 

Kilindini Harbour is the main part of the Port of Mombasa, the only international seaport in Kenya and the biggest port in east Africa.

It is managed by the Kenya Ports Authority (KPA), and is an example of a natural geographic phenomenon called a ria, formed millions of years ago when the sea level rose and engulfed a river that was flowing from the mainland.

During World War II, when Kenya was a British colony, Kilindini became the temporary base of the British Eastern Fleet from early 1942 until the Japanese naval threat to Colombo, Ceylon (now Sri Lanka) had been removed. On 29 August 2013, expansion of the port enabled it to handle Panamax Vessels. 

The project was launched in July 2011 at a cost of $82.15 million by the government of Kenya and was carried out by China Roads and Bridge Corporation (CRBC).

The project is to increase the port throughout by 33 percent, consolidating the leading status of Mombasa as well as Kenya in East Africa.