There are worries that the Co Cork town of Clonakilty may suffer from the overnight floods as high tide is due in the town around lunchtime today.
Cork County Council has activated its major emergency plan after parts of the city and county were left under several feet of water following flash floods overnight.
Gardaí are advising that diversions are in place around Clonakilty.
Emergency services and road crews were notifed and put on alert for potential flooding at 4am this morning.
Noel O'Keeffe, the Cork County Engineer, has said although there is concern about Clonakilty, they are hopeful the worst of the rainfall has finished.
Met Eireann reported that 50mm of rain fell between 8pm and 3am on already saturated ground as thunderstorms swept in from the south.
Locally the figure may have been as high as 70mm.
The worst affected areas included Douglas on the outskirts of the city, Carrigaline, Blackpool, Togher, the Kinsale Road and a stretch of the South Ring Road.
Council chiefs have put a flood response plan in place.
Forecasters warned there will be further rain today but it is not expected to be as heavy as overnight.
Elsewhere there were reports of more than 1,000 homes in Cork without electricity.
The Met Eireann forecast for today is for a band of heavy rain, with embedded thunderstorm activity and hail, to continue to move northwards this morning producing further flooding.
Drier weather will follow with some sunny spells developing, it said.
Meanwhile, flash flooding in Belfast has caused some motorists to abandon their cars.
Heavy downpours last night left many of the main roads in the east and the south of the city impassable.
It is still raining and the Met Office has issued a further amber weather warning.