Major flood alerts were issued as areas battered by Storm Ellen's violent 143kmh winds now face the threat of torrential rainfall over the next 36 hours.
The flood warning centres on south Leinster and Munster, with Cork, in particular, facing another two days of potential water-related damage.
It came as almost 200,000 people were left without power supplies after Storm Ellen tore down trees and damaged property with violent wind gusts.
Taoiseach Micheál Martin paid tribute to the emergency services for "the courage and professionalism they displayed in dealing with a very dangerous storm and, in particular, the hard work of ESB repair crews".
Mr Martin later visited Skibbereen to view the flood damage at first hand and meet the property owners involved on Bridge Street.
ESB officials said it was the third most severe storm of modern times after Storm Ophelia and Storm Darwin, given the scale of the damage sustained by the national power network.
Around 60 ESB repair crews were deployed, but they were only able to commence repair work once it was safe to do so.
Some householders were warned it could be days before they are reconnected. Most were expected to have supply restored by yesterday evening, with 90,000 reconnected by 1pm.
Met Éireann said their concern is now on the heavy rainfall likely to be dumped on Ireland by the Atlantic fronts following Storm Ellen.
They issued a Status Yellow rainfall warning for the entire country and a Status Yellow wind warning for Dublin, Louth, Wexford, Wicklow, Meath, Cork, Kerry and Waterford, with both warnings valid until 5am today.
With rivers and streams already swollen, the flood threat was assessed as extremely serious in some areas.
The Rosscarbery area of Cork has already received 230mm - more than a month's worth - of rainfall in just 72 hours last week.
Cork city was placed on flood alert, given high astronomical tides and the lingering storm surge.
In west Cork, areas including Rosscarbery, Skibbereen and Bandon were again on high alert for flooding.
Twenty properties on Bridge Street in Skibbereen were left under flood waters on Wednesday night.
Officials stressed that it was completely unconnected to an €18m flood relief scheme focused on the River Ilen completed three years ago.
Cork County Council had identified a potential rainfall run-off issue at an area known as The Cutting and a special drain was being built, but it had not yet been completed.
Councillor Karen Coakley said she felt like crying when she saw the damage caused to Skibbereen homes and businesses. "My own home was damaged by floods in 2009 so I know what it is like," she said.
Other Cork towns to be hit by flooding included Midleton, Bantry, Kinsale, Ballinacurra and rural parts of Rosscarbery.
Storm damage - mostly from fallen trees and spot flooding - was also reported in Tipperary, Kerry, Westmeath, Galway, Longford, Kildare and Dublin.
In Clonmel, a parked car was damaged when a tree fell on it.
Cork City Council received almost 40 calls about fallen trees and storm debris, including a large hoarding which was torn down in the city centre and thrown onto a busy roadway.
Multiple roads were left impassable by fallen trees and both the Garda and Road Safety Authority (RSA) pleaded with motorists to be careful of storm-related debris while driving.
Local authority crews were also deployed across Munster to deal with multiple fallen trees which have blocked roads.
In Cork city a giant Monkey Puzzle tree - a famous local landmark for half a century - narrowly missed falling onto a busy roadway by the South Link Road.
A yacht moored in Cobh was swept off its mooring, while, again in Cork, an articulated lorry was flipped onto its side by violent winds.
Storm Ellen even hit water supplies, with Irish Water and Cork County Council working to restore supplies to customers in a number of areas across the county hit by violent winds.
Cork Fire Brigade also had to go to the assistance of a pregnant woman who needed to be rushed to Cork University Maternity Hospital at the height of Storm Ellen.