Met Eireann also has a status yellow gale warning alert in place.
Southerly winds will be light to moderate for most of the night, but towards dawn winds will become southeast and increase fresh to strong in the south.
The forecasters issued a weather warning as an electrical storm with lightning was reported in mid Cork and flood barriers in north Cork held against the surging River Blackwater.
The lightning storm resulted in power outages in the Macroom and Beal na mBlath areas.
Traders and householders in Cork city have been warned that there is a risk of flooding due to the combination of high tides and the swollen state of the River Lee due to recent rainfall.
Localised flood warnings were issued in Cork, Galway, Roscommon, Tipperary and Waterford as winds eased but the risk of flooding increased.
A landslide at Legan, outside Thomastown in Kilkenny, forced the temporary closure of the Kilkenny-Waterford rail line.
Iarnrod Eireann warned passengers that bus transfers will remain in place until the landslide is cleared and the line is inspected.
Met Eireann warned that rivers are being swollen by torrential rainfall which fell over the previous week and was now flowing towards the sea from higher ground.
Weather forecasters also warned that Ireland faces further heavy and possibly thundery showers over the next 10 days.
A ‘yellow status’ gale warning remains in place for waters off Ireland.
The Road Safety Authority (RSA) pleaded with motorists to drive with caution given the amount of ‘spot’ flooding on rural and regional roads.
Flood barriers in Fermoy and Mallow prevented homes and businesses from being hit by flood waters from the River Blackwater.
However, floods still forced the closure of the Mill Road in Fermoy and the Park Road in Mallow.