Roads in Cork and Waterford became impassable in some cases due to the volume of water which had accumulated.
Late last night a number of units of Cork City fire brigade were dealing with flooding in the Blackpool area of the city and in the suburb of Glanmire there were fears of a repeat of the damaging flooding of last June.
Gardaí confirmed that College Rd and Curraheen in the city and a section of Douglas village were also experiencing problems.
Meanwhile, the weather caused severe disruption at Cork Airport with two morning flights from Manchester diverted to Kerry, and two outbound flights — one to Bristol and the other to Edinburgh — cancelled at the last minute.
All the affected flights were operated by Aer Arann using ATR prop aircraft. They were unable to operate safely in the low cloud and poor visibility, which was compounded by strong crosswinds.
The severe weather forced both EI3721 and EI3700 to divert to Kerry with all passengers bussed to Cork.
The 10.45am flight from Cork to Edinburgh and the 11.15am flight to Bristol were also cancelled. Most Bristol-bound passengers were accommodated on Heathrow services and bussed to Bristol.
The passengers on the Edinburgh flight were accommodated on a later Dublin flight.
Frances Dooling, from Cork, was due to fly to Edinburgh with her daughter to visit friends.
“I have never had a flight cancelled before and when it happens you need to be told what is happening. They have been very poor.”
A spokesman for Aer Lingus Regional apologised to customers and said the airline did everything possible to minimise any further disruption to their travel plans.
Dozens of commuters on Irish Rail services to and from Tralee, Cork, and Limerick had to scrap travel plans after they were hit with two-hour delays.