Nagasaki and Nishisonogi Peninsulas are located within the city limits. The city is surrounded by the cities of Isahaya and Saikai, and the towns of Togitsu and Nagayo in Nishisonogi District.
Nagasaki lies at the head of a long bay which forms the best natural harbor on the island of Kyūshū. The main commercial and residential area of the city lies on a small plain near the end of the bay. Two rivers divided by a mountain spur form the two main valleys in which the city lies. The heavily built-up area of the city is confined by the terrain to less than 4 square miles (10 km2).