A search has resumed for a man missing in the waters off Brisbane following the discovery of an unmanned boat.

Queensland police said an empty boat was seen motoring 100 metres off Mud Island, near the Port of Brisbane, about 3.30pm on Wednesday.

The boat is believed to belong to 26-year-old Brisbane man Trent Riley, who has not been seen in more than 16 hours.

Brisbane man Trent Riley is believed to have fallen from his boat in Moreton Bay.

Police believe he fell off his boat.

Water police, the police helicopter, Volunteer Marine Rescue and the Coast Guard searched for Mr Riley late into Wednesday night but found no sign of him.

Ten search boats and three helicopters were involved in the renewed search that began on Thursday morning.

Mr Riley is Caucasian, about 183 centimetres tall, with a proportionate build and brown hair.

It is believed he was wearing a long-sleeved grey fishing shirt, black jeans, black shoes and a bucket hat.

-with AAP