Emergency crews and croc catchers are searching a Top End river where a Darwin man was taken by a crocodile while swimming.

The 24-year-old man was swimming with a friend this afternoon near the Mary River Wilderness Retreat, about 110 kilometres east of Darwin, when a crocodile attacked.

Staff at the holiday park say the man was warned not to swim in the water.

The wilderness retreat's Erin Bayard says crocodiles are very common in the Mary River.

"We do actually tell all our guests not to swim and to stay at least five metres back from the edge of the bank," she said.

Croc catchers have arrived at the site and begun searching for the man.