A number of streets and quays have been closed, however the city has avoided the same damage to homes and businesses that it suffered in October.
Around 100 Council staff were deployed this morning to assist with any clean up efforts.
High tide passed at 06:20 and the majority of flood waters are expected to recede in the next hour.
Director of Services with Cork City Council is David Joyce - he says the waters didn't get as high as predicted:
"We were extremely lucky this morning, up to two hours before high tide, there was gale force winds. They have dropped off which meant we did not peak at 2.8 that we were expecting. We peaked about 2.6, which meant the flooding was significantly less. We did have some traffic disruption, we did have some of the low lying quays were affected, but overall we did not have significant flooding in the city centre this morning."
Council crews are also on call in the County.
One unit of the fire service from Bantry is dealing with a flood in the town square.
A status Orange Wind warning remains in place for Cork until 9am.
