According to Robert Renny's 'An History of Jamaica' (1807):
All the wharves sunk at once, and in the space of two minutes, nine-tenths of the city were covered with water, which was raised to such a height, that it entered the uppermost rooms of the few houses which were left standing. The tops of the highest houses, were visible in the water, and surrounded by the masts of vessels, which had been sunk along with them.
Two-thirds of the town sank into the sea immediately. During the quake, the sand that Port Royal was built on liquefied, so that the buildings seemed to flow into the sea.
The Port Royal Project is a diving excavation project working on the ruins, which still lie off the coast of Jamaica.