The South Alligator River flows through Kakadu National Park in Australia's Northern Territory, roughly a two-hour drive from Darwin via the Arnhem Highway. It is the first major feature encountered when approaching Kakadu from that direction, and the river serves as both a fishing destination and a waterway for general boating and cruising.

The river is a tidal system with significant mud banks and sandbars that extend into the channel. Paddlers need to pay close attention to tidal cycles, as getting stranded on a sandbar or mud bank at low tide is a genuine risk. The waterway is also home to saltwater crocodiles — a serious and constant hazard — and all visitors are strongly advised to follow Crocwise safety practices near and on the water at all times.

The surrounding landscape is characterized by expansive wetlands, monsoon forest, and woodland. Birdlife is abundant throughout the region, and the billabongs connected to the river system — including Alligator Billabong, Bucket Billabong, Red Lily Billabong, Two Mile Hole, and Four Mile Hole — offer additional wildlife viewing opportunities. Mosquitoes can be extremely intense, particularly around dusk, and adequate insect protection is essential.

Barramundi fishing is the primary draw for many visitors, with the season running from February to November. The river is accessible year-round from the main boat ramp, though a 4WD track leading to more remote billabongs in the region is open during the dry season only. The dry season generally aligns with the cooler months and is considered the more practical time for extended trips on the water.

Facilities at the South Alligator area include a boat ramp. The broader South Alligator region within Kakadu National Park also offers camping options. Visitors should be aware that Kakadu National Park requires an entry pass.