Met Eireann has warned that an orange wind warning alert is in place today.
Counties along the East - and county Kerry - will experience gusts of up to 115 kilmometres per hour today.
Another Atlantic storm depression will approach Ireland later today and tonight. Southeast to east winds of mean speeds 65 to 80kmph are expected, and Met Eireann says they will gust 90 to 115 kmph at times, along southern and eastern coasts.
Large waves, high tides and low pressure values are likely to lead to some coastal flooding.
Heavy rain or showers are also expected and with the water table so high, some river flooding is likely too.
A yellow wind warning is in place for Connacht, Cavan, Monaghan, Donegal, Carlow, Kildare, Kilkenny, Laois, Longford, Offaly, Westmeath, Clare, Limerick and Tipperary
Meanwhile, Finance Minister Michael Noonan has pledged to provide additional funding to assist those affected by the devastating floods.
Mr Noonan today visited homes and businesses in Limerick, which have been impacted by the torrential weather.
After an initial early high tide, it's now hoped that the worst of the flooding is over.
Speaking in Limerick, Mr Noonan said that extra funding will be made available to families who have been forced to leave their homes.
"If extra money is needed, we will provide it," he said.
"When we know what the total cost is across the country, we'll provide the funds," he added.
Senior coalition figures have insisted that the €10m government fund, designed to assist householders who do not have insurance, is far from adequate.
Minister of State with responsibility for the Office of Public Works, Brian Hayes, is expected to tell ministers that a "significant" tranche of funding is required.
"It's a terrible situation that people are in… Every government department and the local authorities must work together to ensure that people never, ever have to go through this again," he said.
Another 48 hours of heavy rain have been predicted by forecasters while emergency crews continue to battle with the elements across the country.
Limerick, Clare, Cork, Waterford and Kerry suffered the worst damage in the country and new records were set for both rainfall and floods.
Met Eireann warned that a new storm driven by gale-force winds, heavy rain and new high tides will hit the country tomorrow night.
An Orange Alert was in effect around the country today.
In Cork, flooding was reported in the city and in Bandon, Skibbereen, Mallow and Carrigaline as the county endured torrential rainfall for over 12 hours.
Severe flooding also hit Waterford. Some parts of the city centre were impassable and several city quay car parks were left underwater as the Suir broke its banks due to the storm surge.
Motorists in New Ross were held up for four hours at one stage as the floods caused traffic chaos.
Flooding almost cut the Kilmeaden to Carrick-on-Suir road while Tramore's promenade was again left underwater - having been so three weeks ago.
Meanwhile, a flood alert has been issued in Athlone, amid fears houses in low-lying areas of the town could be hit later this week.
High winds and heavy rain are set to continue until this evening and Met Eireann has warned that the risk of flooding will continue until the middle of this week.
Homeowners will have a short break from the showers today but the heavy rain will continue this week leaving many areas at risk of flooding.
"There will be a short break today but the wet and windy weather will continue on Tuesday and Wednesday leaving some areas at risk of flooding,’’ Met Eireann forecaster Tim O’Brien said.
The forecaster was unable to determine the areas most at risk of flooding as it will depend on high tides and wind direction.
"The high tides in Cork have passed so it may ease up for today,’’ he said.
The forecaster said water will begin to recede in devastated areas in Limerick and Cork but the areas will still be at risk of flooding during the week.
He said Co. Waterford may be at risk today as southerly winds and wet weather in the east may induce flooding.
New Ross Garda station in Co Wexford has also been hit by rising water levels.
An Garda Síochána have warned motorists to take care while driving.
‘‘There is heavy rain throughout the country's road network, take care & watch for flooding and surface water, slow down, light up, drive safe,’’ it tweeted.
A main road in Inishmore was completely demolished after high tides crashed against the coastline, leaving locals cut off from diesel pumps and a recycling centre.
‘‘It’s likely that we won’t be able to get oil to heat homes. That’s what happened the last time,’’ said Cathy Gill of the island’s local cooperative.
‘‘The initial damage was done during the last floods and now it’s just been made worst and there’s nothing to stop it.
‘‘We have been devastated this time round,’’ she added.
James Ring woke up to find almost nine feet of water in his back garden and spoke of how ‘‘frightening’’ it was.
“Saturday morning we woke to find literally a wall of water surging towards our house,’’ he told Morning Ireland on RTÉ Radio 1.
“When I opened the blinds of the back door of my house I saw a four and a half foot wall of water looking back at me,” he explained.
“As you can imagine it was quite frightening.”
He said the flooding happened so quickly that householders in the area in Limerick had no chance to prevent the damage.
“All we could do was pick up a couple of things and run from our home.
“The house is destroyed. We live in terraced bungalows so literally every room in our house is destroyed,” he said.
Parts of Co. Limerick were severely flooded when the Shannon burst its banks on Saturday.
He explained how water poured out of sockets in the walls.
The homeowner insisted that his insurance would not cover the damage.
“I pay over €600 a year for insurance and the problem is that we can’t get insurance for floods.
“That’s the problem that we’re faced with now.
“What’s causing such panic in the community is that people just don’t know what way to turn,’’ he added.
The flood victim called on the state to provide financial help to those affected by the flood damage.
‘‘This is a disaster zone. We’re talking numbers in the thousands here being affected,’’ he said.
He called for Taoiseach Enda Kenny to travel to Limerick to see the damage.
Mr Ring was woken by his neighbour after she thought her tank had burst after her kitchen was flooded.
He went into his panicked neighbour’s house to check the tank.
‘‘When I opened the windows, I saw this surge of water running through the gardens,’’ he said.
He warned his neighbour to leave the house immediately before fleeing from his own home after waking his girlfriend.
Junior Minister Brian Hayes is travelling to the region this morning to inspect the damage.
High tide occurs again tonight at around 8pm in the region.
Meanwhile high winds and storm tides caused flood misery with the River Lee breaking its banks in Cork for the second time in three days.
Worst hit was Oliver Plunkett Street where drains swamped with heavy rainfall couldn't cope with the additional demands of the high tide leaving the busy shopping street resembling a river with some shops under 45cm of water.
Claire Nash of Nash 19 bistro said the floods were the worst since the 2009 disaster when a quay wall collapsed.
"A few of my neighbours were badly hit. I was lucky in that I had a flood gate and measures that we put in place after 2009 helped protect the premises. But we are still mopping out this morning," she said.
Amongst the worst hit shops were John Joyce's leisure outlet, Ruiseal's Bookshop and Finbarr Cotter's Newbridge Silverware.
Chemist and former Progressive Democrat senator, John Minihan, warned that flood protection measures now need to be fast-tracked as a matter of urgency.
The combination of high tides, torrential rainfall and south-westerly winds resulted in flooding throughout low-lying parts of Cork city centre from 7.20am (Monday).
Flooding resulted in lane closures along several city centre roads with heavy flooding on Fr Mathew Quay, South Mall, the Lower Glanmire Road, Morrisson’s Quay, Union Quay, Lavitts Quay and Wandsford Quay.
Niall O'Connor, Aishling Phelan and Ralph Riegel