The Johnstone River is a river system in Far North Queensland, Australia, comprising two main branches — the North Johnstone River and the South Johnstone River — which converge near the town of Innisfail before emptying into the Pacific Ocean. The river originates on the Atherton Tableland, with the North Johnstone's headwaters sitting at approximately 760 metres elevation in Palmerston National Park. The system is subject to periodic flooding and is well known for whitewater paddling.

The North Johnstone is the more demanding of the two branches, rated Class IV-V and consistently regarded as one of Australia's most challenging whitewater runs and one of the top rafting trips in the world. The put-in is accessible only by helicopter from a staging point roughly two hours' drive from Cairns, and trips run four to six days through a deep canyon flanked by World Heritage-listed rainforest. Rapids along the route carry names such as Mordor, Mineshaft, and Misjudgement, and each requires careful scouting or portaging. The remoteness of the canyon means paddler traffic is extremely low. The North Johnstone is only suitable for highly experienced paddlers; the river is unpredictable and has claimed lives. The recommended season is April through June, as the river is undammed and flow is dependent on winter rainfall.

The South Johnstone offers a different character, with sections of Grade II+ water accessible via a fishing trail that leads into the river downstream of the Grade IV+ upper reaches, providing at least 15 kilometres of more moderate paddling. Access and egress on the South Johnstone are complicated by the prevalence of banana plantations along the banks; much of the riparian land is under quarantine due to Panama Disease, restricting take-out options largely to public access points such as bridges, which are spaced well apart.

A significant hazard on both branches is the presence of saltwater crocodiles, which must be factored into all trip planning. Feral pigs have also been noted in the surrounding terrain. The landscape throughout the system is dense tropical rainforest, and the river corridor provides habitat for diverse wildlife. Fishing species recorded in the system include barramundi, sooty grunter, and giant trevally. The junction of the two river branches holds cultural significance as a sacred site for the indigenous Mamu people.