Kilindini Harbour, Natural deep-water port in Mombasa, Kenya.

Kilindini Harbour is a natural deep-water inlet that reaches inland from Mombasa, with depths of 25–30 fathoms (46–55 m) at its deepest centre, while the dredged outer approach channel is 17.5 m. It forms the main part of the Port of Mombasa, Kenya's only international seaport, and is managed by the Kenya Ports Authority. A new berth, Berth 19, with 6.1 ha of stacking yard, was added in the 2011–2013 expansion.

The port opened in 1896 during construction of the Uganda Railway and later took on military importance. It served as a British Eastern Fleet base during 1942 in the Second World War.

Kilindini is Swahili for "deep down" or "in the depths", referring to the channel's depth. The port also welcomes cruise ships alongside cargo vessels, and its hinterland reaches landlocked Uganda, so goods for that country pass through here.

The harbor is visible from various points in the city and offers spots where you can watch the ships. Note that some port areas are restricted for security reasons and not all sections are open to the public.

Kilindini is a ria: a river valley drowned when the sea rose, which is why the inlet reaches 46–55 m at its deepest centre. The name is Swahili for "deep down" or "in the depths", referring to that channel. The approach channel is dredged to 17.5 m, so the deepest water lies inside rather than at the entrance.