They were explored by Lieutenant Phillip Parker King in 1820, who named them in the mistaken belief that the crocodiles in the estuaries were alligators.

After rising in the northern part of the Arnhem Land Plateau, it flows with tributary streams towards the northwest, through canyons towards the Van Diemen Gulf, which it meets at Point Farewell.

The rivers have created the alluvial plains, including the mangrove swamps, in the past 20,000 years.

The land dries out, and the wildlife concentrates around the permanent water sources such as the rivers, springs, waterholes, and billabongs.

The region also features high populations of the dusky rat and its predator the water python.

Invasive species such as feral water buffalo and cane toads are also causing problems.

In particular, the Alligator Rivers area is known for its rich collection of waterfowl such as magpie geese, ducks, herons, ibises, and spoonbills.

At Ubirr Rock near Cahill's Crossing on the East Alligator River, some paintings dating from 20,000 years ago have figures throwing spears and wearing headdresses to first contact with European settlement.

Gunbalanya (formerly Oenpelli), a settlement in the area, is run by an Aboriginal council and is an important centre for arts and crafts.

He made a number of explorations in the area between 1818 and 1822 and named the rivers after the crocodiles which he mistook for alligators as his journals note.

This was the first time we had seen these animals, excepting that at Goulburn Island, and, as they appeared to be very numerous and large, it was not thought safe to stop all night up the River.

"[9] Ludwig Leichhardt was the first European explorer to visit the area in 1845 en route to Port Essington.

Leichhardt followed a creek down from the Arnhem Land escarpment before crossing the South and East Alligator Rivers.

Paddy Cahill, who came to the area to set up a cattle station, was the first buffalo hunter to operate in the region.

The Kapalga Native Industrial Mission was established in 1899 near the South Alligator River, but only lasted four years.

The Church of England Missionary Society established a mission station in 1925 at Oenpelli which lasted for 45 years.

Small-scale gold mining started in the region in the 1920s at Imarlkba near Barramundi Creek and at Moline in the 1930s.

However, the discovery of uranium at the headlands of the South Alligator River in 1953 started the mining industries.