It looks like the sea level for the northern side of the Mediterranean increased by about 1.5 meters since Roman times, due to isostatic rebound: http://people.rses.anu.edu.au/lambeck_k/pdf/242.pdf

The wikipedia page for Heracleion attributes it to "soil liquefaction", i.e. the whole city's underlying soft soil/sand became fluid enough to wash away. It must have been eroded to other parts of the sea, leaving the inerodible stoneworks lying there.

It even increased by 2500m in the last 6 million years. The Nile cut at Cairo into a huge canyon. This area is constantly sinking. https://en.m.wikipedia.org/wiki/Messinian_salinity_crisis