West Cork was badly hit in the early stages of the red warning coming into place, according to the County Council.
Pumping operations are underway in Bantry where the square has flooded. Streets in Youghal and Midleton have also been hit by flooding this morning
Senior Engineer John Donegan says Bantry in particular has been severely impacted .
"We're in a period of spring tides, with coastal surge of up to a metre.
"The sea wall has been over topped, and the culvert that runs through the centre of the town has been surcharged, resulting in up to 20-25 properties being flooded."