The island largely consists of dense jungle and mountains, reaching its highest point at Mt. Kinabalu (13,455 ft/4,101 m) in Sabah. Much of the terrain is virtually impassable, and large areas are unexplored. Many of the rivers are navigable to small craft, however, and provide access into the interior. The largest rivers are the Kapuas in the west and the Barito in the south. The coastal area is generally swampy and fringed with mangrove forests. Banjarmasin, Pontianak, Balikpapan, Tarakan, Kuching, Bandar Seri Begawan, and Sandakan are leading ports. The climate is tropical, i.e., hot and humid; annual rainfall averages more than 100 in. (254 cm), and there is a prolonged monsoon (generally from November to May). The fauna is roughly similar to that of Sumatra and includes the elephant, deer, orangutan, gibbon, Malay bear, and crocodile, and many varieties of snakes. Rhinoceroses, once numerous, have been extensively hunted and are now almost extinct.

The island is one of the most sparsely populated regions in the world. The two major ethnic groups are the Dyaks and the coastal Malays. Kalimantan was also a center for Chinese settlement and has a number of immigrants resettled during the second half of the 20th cent. from overcrowded areas of Indonesia, particularly Madura.

The Borneo rainforest is 130 million years old, making it the oldest rainforest in the world and 70 million years older than the Amazon rainforest. Borneo is very rich in biodiversity compared to many other areas (MacKinnon et al. 1998). There are about 15,000 species of flowering plants with 3,000 species of trees (267 species are dipterocarps), 221 species of terrestrial mammals and 420 species of resident birds in Borneo (MacKinnon et al. 1998). It is also the centre of evolution and radiation of many endemic species of plants and animals. Subject to mass deforestation, the remaining Borneo rainforest is one of the only remaining natural habitat for the endangered Bornean Orangutan. It is also an important refuge for many endemic forest species, as the Asian Elephant, the Sumatran Rhinoceros, the Bornean Clouded Leopard, the rare Hose's Civet and the Dayak Fruit Bat. An important reserve for elephants and rhinos is Tabin Wildlife Reserve in the northeastern corner of Borneo.

It is one of the most biodiverse places on earth. The World Wildlife Fund has stated that 361 animal and plant species have been discovered in Borneo since 1996, underscoring its unparalleled biodiversity. In the 18 month period from July 2005 until December 2006, another 52 new species were found.

The World Wildlife Fund divides the island into seven distinct ecoregions. The Borneo lowland rain forests cover most of the island, with an area of 427,500 square kilometres (165,100 sq mi). Other lowland ecoregions are the Borneo peat swamp forests, the Kerangas or Sundaland heath forests, the Southwest Borneo freshwater swamp forests, and the Sunda Shelf mangroves. The Borneo mountain rain forests lie in the central highlands of the island, above the 1,000 metres (3,300 ft) elevation. The highest elevations of Mount Kinabalu are home to the Kinabalu mountain alpine meadow, an alpine shrubland notable for its numerous endemic species, including many orchids.

The island historically had extensive rainforest cover, but the area shrank rapidly due to heavy logging for the needs of the Malaysian plywood industry. Two forestry researchers of Sepilok Research Centre, Sandakan, Sabah in the early '80s identified four fast-growing hardwoods and a breakthrough on seed collection and handling of Acacia mangium and Gmelina arborea, a fast growing tropical trees were planted on huge tract of formerly logged and deforested areas primarily in the northern part of Borneo Island. Half of the annual global tropical timber acquisition comes from Borneo. Furthermore, Palm oil plantations are rapidly encroaching on the last remnants of primary rainforest. The rainforest was also greatly destroyed from the forest fires of 1997 to 1998, which were started by the locals to clear the forests for crops and perpetuated by an exceptionally dry El Niño season during that period. During the great fire, hotspots could be seen on satellite images and the haze thus created affected the surrounding countries of Brunei, Malaysia, Indonesia and Singapore. In February 2008, the Malaysian government announced the Sarawak Corridor of Renewable Energy plan[18] to harvest the virgin hinterlands of Northern Borneo. Further deforestation and destruction of the biodiversity are anticipated in the wake of logging commissions, hydroelectric dams and other mining of minerals and resources.

In order to combat overpopulation in Java, the Indonesian government started a massive transmigration (transmigrasi) of poor farmers and landless peasants into Borneo in the 70s and 80s, to farm the logged areas, albeit with little success as the fertility of the land has been removed with the trees and what soil remains is washed away in tropical downpours.

Kalimantan contains Indonesia's greatest expanse of tropical rain forests, including valuable stands of camphor, sandalwood, and ironwood, and many palms. The thick jungle and myriad insects tend to discourage large-scale agriculture, but rice, sago, tobacco, millet, coconuts, pepper, sweet potatoes, sugarcane, coffee, and rubber are grown. In 1983, over 13,000 sq mi (20,917 sq km) of rain forest were destroyed by fire, causing enormous damage to the ecosystem, and immigration from other, heavily populated parts of Indonesia, combined with illegal logging, has resulted in increasing deforestation, threatening the orangutan, the pygmy elephant, and other species. Kalimantan contains some of Indonesia's most productive oil fields (discovered in 1888). Coal has been mined there for more than a century, and gold since earliest times. In 1995 one of the richest gold deposits in the world was discovered in NE Kalimantan. Other mineral resources include industrial diamonds, bauxite, and extensive reserves of low-grade iron ore, which are, however, little exploited.

Brooke took the north edge of the island in the 1840s, and what is now Sabah was declared a British protectorate in 1882, Sarawak and Brunei in 1888. The final boundaries were defined in 1905. In World War II the island was held by the Japanese from 1942 to 1945. Dutch Borneo became part of the republic of Indonesia in 1950. The union of Sabah and Sarawak with Malaya in the Federation of Malaysia in 1963 was resented by Indonesians. Indonesian guerrilla raids against both areas, begun in 1964, continued sporadically until Aug., 1966. The sultanate of Brunei became fully independent in 1984. The resettlement of non-Dyak Indonesians in Kalimantan has led to recurrent violence against the settlers by Dyaks.

Borneo has a typical equatorial climate with sunshine all year round. Temperatures are fairly uniform, averaging 25-33 degrees Celsius during the day and rarely dropping below 20 degrees Celsius at night, except in the mountains where they can drop to below 20 degrees Celsius. Most rainfall occurs between November and January during the northeast monsoon, and is characterised by sharp cloudbursts which are short in duration. The dry season runs form May to September.