It flows 980 kilometers (610 miles) from the district of Long Apari in the highlands of Borneo, to its mouth at the Makassar Strait.

The city of Samarinda, the provincial capital of East Kalimantan, lies along 48 kilometers (30 mi) from the river mouth.

The delta Mahakam river consist of specific micro climate which is influenced by high and low tide at sea level.

From there, the river flows eastward through the Mahakam lakes region, which is a flat tropical lowland area surrounded by peat land.

[10] According to Köppen climate classification, this area belongs to type Af (tropical rainforest) and has a minimum temperature ≥18 °C and precipitation of the driest month in normal year ≥60 mm[11] Transfer of mass and energy in the tropical zone occurred through general air circulation known as the Hadley cell.

This circulation carries moisture into the air, generating rainfall in equatorial regions, whereas the edges of the tropical belt are drier.

[12] Within this circulation, evaporation occurs intensively around the equator on the center of low pressure called the Intertropical Convergence Zone (ITCZ), characterized by the accumulation of clouds in the area.

The ITCZ drives the Indo-Australian monsoon phenomena which influence the regional climate including the Mahakam catchment.

[32] This lower Mahakam area is the second most productive hydrocarbon basin of Indonesia which contains around 3 billion barrels of oil and 30 Tcf of gas reserves.

[33] Field geological investigations in this area were started in 1888 and in 1897 exploration drilling discovered oil at a shallow depth of 46 meters (151 ft) on the Louise structure.

[35] The Mahakam hosts the freshwater dolphin Irrawaddy dolphin (Orcaella brevirostris; called Pesut by local people) a critically endangered species, which is included in CITES (Convention on International Trade in Endangered Species of Wild Fauna and Flora) Appendix I.

The cluster's objective is to study the impact of external forcing factors such as sea-level rise, climate change, upstream sediment, as well as human interference on past, present, and future development of the Mahakam delta in different time scales.

Logging and mining activities have contributed to the "alarming rate" of pollution of East Kalimantan's Mahakam River.

The River Mahakam is an economic resource for fishermen and farmers and a freshwater source, as a waterway since ancient times until today.

In around 1565, Islam was extensively spread in Kartanegara by two Moslem preachers from Java, Tunggang Parangan and Ri Bandang.