The South Alligator River runs approximately 160 kilometres through the heart of Kakadu National Park in the Northern Territory of Australia. Rising near Mount Stow on the Arnhem Land Plateau, it flows northwesterly before emptying into the Van Diemen Gulf of the Timor Sea. Its catchment area covers 11,917 square kilometres. The entire river and its catchment are contained within Kakadu National Park, which holds dual UNESCO World Heritage listing for both its natural and cultural values.

The primary access point for boating and paddling is located near the South Alligator Bridge on the Arnhem Highway, where a boat ramp, picnic tables, and fish cleaning facilities are available. The nearby Aurora South Alligator (formerly Kakadu Resort) provides fuel, a general store, meals, and other amenities. Paddlers heading downstream toward the river mouth should be aware of mud banks and sandbars that extend into the river, which can cause vessels to become stranded at low tide. The trip to the river mouth is described as a long journey requiring appropriate safety gear and a suitably sized vessel.

The most significant safety concern on the South Alligator River is the presence of saltwater crocodiles. Crocodile warning signs are posted throughout the area and must be observed. This is a genuine hazard that demands constant vigilance near and on the water.

The dry season is the primary period for accessing the river and surrounding areas. During the dry season, 4WD tracks open to remote locations such as Two Mile Hole, Four Mile Hole, and Red Lily Billabong, which offer additional boating and bird-watching opportunities. Barramundi fishing is active from February to November, with the run-off season of February to April considered the most productive period, coinciding with the wet-to-dry transition.

The river flows through a landscape of exceptional biological richness, regarded as one of the most diverse in Australia. The adjacent Mamukala wetlands support a wide variety of birdlife, observable from a dedicated platform and dry-season walking track. The broader Alligator Rivers region also contains over 1,500 Aboriginal rock art sites, reflecting deep cultural and historical significance. Camping is permitted in designated areas only.