The Whakapapa River originates on the slopes of Mt Ruapehu in Tongariro National Park and flows northward, eventually joining the Whanganui River near the village of Kakahi. The river is formed by the confluence of two tributaries, the Whakapapaiti and the Whakapapanui, below the Whakapapa Dam. The riverbed is bouldery with an even gradient, and the surrounding banks are lined with native New Zealand podocarp forest, including some of the tallest stands of rimu and kahikatea in the country. The area supports the highest density population of whio (blue duck) in New Zealand, making wildlife encounters a regular feature of any paddle.

The main whitewater run extends from the Whakapapa intake structure (below the Whakapapa Dam) to the bridge at Owhango, covering approximately 23 kilometres and typically taking four to six hours. This section is rated Grade 3–4, with optimal flows between 25 and 60 cumecs. The shuttle is approximately 40 kilometres. The character of this run is described as wilderness, scenic, and relatively consistent in gradient. Note that the Tongariro Power Scheme controls water releases, and the river is known to run at its best on scheduled release days — historically around two per year in September — when the power company is not diverting water. Below 25 cumecs the run becomes scratchy; above 60 cumecs the river becomes a demanding, committing experience with limited escape options.

The two tributary runs above the dam offer additional options. The Whakapapanui (SH47 road bridge to Whakapapa Dam, 9 km, Grade 3–4) is considered the more scenic and slightly more forgiving of the two. The Whakapapaiti (SH47 to Whakapapa Dam, 9 km, Grade 3–4) is faster and more technical. Both are rain-dependent due to their small catchments and are best run between 20 and 50 cumecs.

A lower, more accessible section near Owhango is used by guided commercial operators running half-day trips in two-person inflatable kayaks, covering roughly 9 kilometres before joining the Whanganui River. This section features Grade 2–3 rapids and is suitable for beginners and families. Access to the upper reaches via Intake Road has at times been subject to closure disputes, so paddlers should verify current access status before planning a trip. Access to the lower reaches is available from the end of Te Rena Road via Kakahi.