It originates in the Müller Mountain Range at the center of the island and flows south until merging with the Barito River and discharging into the Java Sea.

[4] It should be distinguished from another Kapuas River, which starts on the other side of the same mountain range in central Borneo but flows to the west and empties to the South China Sea.

It flows through a marshy region rich in tropical forests, nearly parallel to the Barito River, and merges with the latter about 60 km from the Java Sea coast, within the town of Kualakapuas (lit.

Between 1880 and 1890, a 30 km long canal was dug by the Dutch colonizers between the Kapuas and Barito rivers for agricultural purposes.

Its discharge rate varies through the year reaching the maximum in the peak of rainy seasons in April and November.