In the center of the valley, it meanders southeast to meet the Uwe River in the town of Wamena, the capital of Highland Papua province.

70 kilometers southeast of Wamena the Heluk River enters the Baliem near Holuwon village.

After 100 kilometers, the Baliem, slightly upstream from the village of Kaima, flows into the Pulau River (formerly the Eilanden River), which flows into the Arafura Sea about 100 kilometers southwest on the Casuarina Coast.

[3][citation needed] The Baliem River has a length of about 60–80 km with a width of 15–20 m, flowing through the town of Wamena.

[4] The acidity level of the Baliem is considered good for the growth of water organisms, such as fish.

Along the banks, there are swamps, with a high tendency of flooding used by the community to let loose their pig herds.