Mombasa County lies within the coastal lowland, which rises gradually from the sea level in the east to slightly over 76 m above sea level in the mainland west. The highest point is at Nguu Tatu hills in the mainland north which rises up to 100 m above sea level.
Mombasa is the capital and the only city in the county of Mombasa. Initially, it was one of the former districts of Kenya but in 2013 it was reconstituted as a county, on the same boundaries. It is the smallest county in Kenya, covering an area of 229.7 km2 excluding 65 km2 of water mass.
The county is situated in the southeastern part of the former Coast Province. It borders Kilifi County to the north, Kwale County to the southwest, and the Indian Ocean to the east.