Kota Kinabalu is located on the west coast of Sabah. The city lies on a narrow flatland between the Crocker Range to the east and the South China Sea to the west. There are six islands off the coast of the city. The largest is Pulau Gaya, the site of the first British settlement. Approximately 8,000 people live there. The smaller islands, mainly uninhabited, are named Pulau Sapi, Pulau Manukan, Pulau Sulug, Pulau Mamutik and Pulau Sepanggar to the north. Sepanggar island is located north of the National Park opposite Sepanggar Bay.

Flat land is at a premium in the city centre, and there is a strict limit to the height of buildings: the airport is 7 km away, and the city is directly in the flight path. Most of the Central Business District (CBD) today is built on land reclaimed from the sea. The original local plant life has largely disappeared, but several hills within the city (too steep for building) are still clothed with tropical rainforest. One of these is Signal Hill, which confines the CBD to the shore.

In the area of Likas Bay the remnants of an extensive mangrove forest was nearly lost. In 1996, a perceptive state government stepped in and declared 24 acres of the forest as a protected area. This forest is now known as the Kota Kinabalu City Bird Sanctuary. The sanctuary was given additional protection as a State Cultural Heritage Site in 1998.

The five islands (of Gaya, Sapi, Manukan, Sulug, Mamutik) opposite the city, and their surrounding waters, are also preserved as the Tunku Abdul Rahman National Park. The park was named in honour the first Prime Minister of Malaysia, Tunku Abdul Rahman. This is a popular recreational spot for tourists and local people.

The Kota Kinabalu city centre, mostly business and government, includes Karamunsing, the port area (Tanjung Lipat), Signal Hill, Kampung Air, Sinsuran, Segama, Asia City, Gaya Street (Old Town), Bandaran Berjaya, Api-Api, Sutera Harbour and Sembulan.

Outlying neighbourhoods and residential suburbs include Kepayan Ridge, Tanjung Aru, Petagas, Kepayan, Lido, Lintas, Nosoob, Bukit Padang, Luyang, Damai, Likas and Kolombong. The city is growing steadily and the urban sprawl extends to the towns of Inanam, Menggatal, Sepanggar, Telipok and south of the district border to Donggongon, Putatan, and Lok Kawi.

Kota Kinabalu is generally isolated from the rest of the country; it is located about 1,624 kilometres (1,009 miles) from Kuala Lumpur in Peninsular Malaysia and 804 kilometres (499 miles) from Kuching in the neighbouring state of Sarawak.

Climate

Kota Kinabalu experiences a typical equatorial climate, with constant temperature, considerable rain and high humidity. Two prevailing monsoons characterise the climate of this part of Sabah, the Northeast Monsoon and the Southwest Monsoon. The Northeast Monsoon occurs between November and March, while the Southwest Monsoon occurs between May and September.

There are also two successive inter-monsoons from April to May and from September to October. Temperature variation throughout the year is small. However, April and May are generally the hottest months, while December and January are often the coolest.

Rainfall varies markedly through the year with February and March are typically the driest months while rainfall peaks in the inter-monsoon period around October. Relatively humidity is high, typically over 80% throughout the year.