A 61-year-old Polish man was discovered face-down and unconscious in the water at Comino's Blue Lagoon this afternoon, police said.
He was lifted to shore and given first aid but was certified dead by a medical team rushed to the site.
Comino police were called to the site at 2.20pm, with the Armed Forces also roped in.
Magistrate Paul Coppini has ordered an inquiry into the case. Police say they are investigating further.