Borneo is surrounded by the South China Sea to the north and northwest, the Sulu Sea to the northeast, the Celebes Sea and the Makassar Strait to the east, and the Java Sea and Karimata Strait to the south. It is the largest island in the Malay archipelago, with an area of 743,330 square kilometres (287,000 sq mi). To the west of Borneo are the Malay Peninsula and Sumatra. To the south is Java. To the east is Sulawesi, and to the northeast, the Philippines.
Borneo's highest point is Mount Kinabalu in Sabah, Malaysia, with an elevation of 4,095 m (13,435 ft) above sea level. It is the third highest peak in South East Asia, making Borneo the world's third highest island.
The largest river system is the Kapuas in West Kalimantan. With a length of 1,143 km (710 mi), it is the longest river in Indonesia. Malaysia's longest river, the Rajang, lies in Sarawak and is 562.5 km (349.5 mi) long. Other major rivers include the Barito in South Kalimantan (880 km long (550 mi)) and the Mahakam in East Kalimantan (980 km long (610 mi)).
Borneo has significant cave systems. Clearwater Cave, for example, has one of the world's longest underground rivers. Deer Cave is home to over three million bats, with guano accumulated to over 100 metres (330 ft) high.