Indonesia consists of 17,508 islands, about 6,000 of which are inhabited. They are scattered over both sides of the equator. The largest are Java, Sumatra, Borneo (shared with Brunei and Malaysia), New Guinea (shared with Papua New Guinea), and Sulawesi. Indonesia shares land borders with Malaysia on Borneo, Papua New Guinea on the island of New Guinea, and East Timor on the island of Timor. Indonesia shares maritime borders across narrow straits with Singapore, Malaysia, and the Philippines to the north, and with Australia to the south. The capital, Jakarta, is on Java and is the nation's largest city, followed by Surabaya, Bandung, Medan, and Semarang.

At 1,919,440 square kilometers (741,050 sq mi), Indonesia is the world's 16th-largest country in terms of land area.

Java is the world's most populated island. At 4,884 metres (16,024 ft), Puncak Jaya in Papua is Indonesia's highest peak, and Lake Toba in Sumatra its largest lake, with an area of 1,145 square kilometers (442 sq mi). The country's largest rivers are in Kalimantan, and include the Mahakam and Barito; such rivers are communication and transport links between the island's river settlements.