01244 and 01829 were among the dialling codes which were affected from 5.34am but BT has confirmed that normal service resumed at 2.42pm this afternoon.
Many homes and businesses experienced disruption with their landlines, including the Countess of Chester Hospital which had difficulties receiving incoming calls.
Cheshire Fire and Rescue Service advised affected residents to dial 999 from a mobile in the event of an emergency.
A spokesman for BT said: "“We wish to apologise to customers for the loss of some telephone services which has been caused by water damage at our exchange in Chester.
"This has affected some customers in parts of North East Wales and Cheshire."
Villagers from Ashton Hayes were without phone lines and broadband connection on more than one occasion last year. They were reconnected just before Christmas having experienced problems during the summer and from November onwards.