Large parts of Arnhem Land in the Northern Territory are under water after Tropical Cyclone Megan unleashed its fury on the region on Saturday.

The cyclone is now expected to intensify today, passing over Groote Eylandt, bringing heavy rains and flooding to the area.

Groote Eylandt has received 431 millimetres of rainfall in the past 24 hours.

The cyclone strengthened into a category two system on Saturday evening and will become category three cyclone by Sunday evening, the Weather Bureau said.

A cyclone warning alert is in place from Groote Eylandt to Mornington Island and as far inland to Borroloola, McArthur River Mine and Robinson River.

Groote Eylandt resident Alia Stevenson told the ABC it was “quite frightening.”

“It was a full torrential downpour. It’s a mess and it’s going to be a lot of work to repair,” she said.

Many residents have been without power and water for 48 hours, but it is believed power has since been restored.

Residents in Gunbalanya, in western Arnhem Land, were evacuated on Friday due to rising floodwaters.