Officials onboard a coastguard boat laid wreaths for the victims at a ceremony held where the disaster took place on March 6, 1987, one kilometre (half a mile) from the Belgian coast.
"It is now 30 years since a story of pain, sorrow and trials was written here. I would like to bow down here in front of those for whom time stopped at this place," said Carl Decaluwe, the governor of western Flanders province.
British ambassador Alison Rose and Decaluwe both cast wreaths into the seawater, while a lone bugle sounded after a minute's silence.
Former rescuers travelled to the site on another boat.
Survivors and family members of the victims meanwhile took part in a ceremony at a memorial set up after the disaster in the town of Zeebrugge.
The Townsend Thoresen ferry the "Herald of Free Enterprise" turned over on its side just outside Zeebrugge as it set out for Dover with more than 500 passengers and crew on board.
A public inquiry confirmed the ferry had left port with its bow doors open, letting water flood the car deck and fatally destabilising the vessel.
The crew member responsible for closing the doors of the ferry was asleep at the time, the investigation found.
In October 1987, an inquest returned verdicts of unlawful killing.
The company -- later rebranded as P&O European Ferries -- was later charged with corporate manslaughter, but there were no convictions.
Heroics saved many lives: those honoured included ex-policeman Andrew Parker, who became known as "the human bridge" for saving his wife, daughter and 20 other passengers whom he let walk over his body to escape.
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