The city wasn't below sea level when it was built. It subsided afterwards. Channelization of the river kept it from being annually flooded and thus kept it from the supply of silt that would have maintained it's height. And the wells sunk by the inhabitants for water drew down the aquifer underneath it, causing the silt bed it was built on to contract.
okie01 was just explaining that. I remember seeing a show about all the lengths they've gone to to force the river on the path they want it to take or something. Best laid plans...