Crowded public ferries are the cheapest way to tackle the Lower and Middle reaches of the Mahakam. Passengers sit on the floor, though night services provide a bedroll on an upper, enclosed, level. Toilets are a simple bucket-and-hole affair at the back; some ferries also serve basic snacks, though hawkers are the main source of food. If you plan to disembark before the boat's ultimate destination, make sure that the pilot, not the ticket collector, knows.

Ferries leave Samarinda's Terminal Sungai Kunjang every morning for towns as far upstream as Long Iram; all services pause for half an hour at Tenggarong, a good alternative starting point. As all ferries depart at roughly the same time, if you get out at any stage you'll have to stop over for 24 hours until the next batch arrive. The following schedule from Samarinda is a guide only and varies according to the weather and number of stops: Tenggarong (3hr; Rp1000); Melak (24hr; Rp8000); Kota Bangun (10hr; Rp3500); Long Iram (30hr; Rp10,000); Muara Muntai (14hr; Rp5000); and Long Bagun (40hr; Rp15,000). To catch a ferry from smaller settlements you stand on the jetty and hail passing traffic.

A more luxurious option for seeing the Mahakam are private houseboats , which can be rented for about Rp150,000 a day through agencies in Samarinda and Balikpapan, and come complete with guides, cooks and private cabins. Away from the water, buses link Samarinda to Tenggarong and Kota Bangun, and are a useful shortcut.