[7] It originates in the Müller mountain range at the center of the island and flows west into the South China Sea creating an extended marshy delta.

[6][9] The river originates near the center of Borneo, south of the Indonesian-Malaysian border, in the joint between the western slope of the Müller Mountain Range, which runs through the island center, and the southern slope of the Upper Kapuas Range (Indonesian: Kapuas Hulu), which is located more to the west.

[11] The delta is located west-southwest of Pontianak, the capital of West Kalimantan province, which lies at the equator.

The discharge peaks during the rainy seasons in April and November, during which the water level may rise by 10–12 m (33–39 ft) overnight, overflowing river banks and flooding the nearby areas.

[22] In the upper and middle reaches, the river flows through dense tropical forests; the rich flora and fauna are the subject of international research.

[9] Discoveries of new species are frequent, such as the Kapuas mud snake (Enhydris gyii), which was discovered in 2003–2005 by German and American herpetologists.

[29] Among the economically important species are food fish such as Pangasius catfish, giant gourami, kissing gourami, snakeheads, and large cyprinids such as Tor mahseers and barbs such as Leptobarbus and Puntioplites, and species for the aquarium trade such as the super red arowana and various rasboras.

Among these endangered species are the arowana and white-edge freshwater whipray, and the wallago catfish, which formerly migrated in large schools up and down the Kapuas River.

In the headwaters are fast-flowing highland streams, typically dominated by small loaches, and small —often acidic (blackwater)— forest streams and peat swamps with species such as the tiny Sundadanio rasboras, Sphaerichthys gouramis, and macropodusine gouramis.

In the deepest sections, no light exists and in one species, Lepidocephalus spectrum, this has resulted in a complete reduction of both eyes and pigmentation (similar to cavefish).

[30] Owing to the warm climate and abundance of food, most fishes breed all through the year with only a few species like fire eel (Mastacembelus erythrotaenia) having certain reproductive periods.

Abundant fruits and seeds enter the river after falling from large trees that bend over its waters.