Householders and businesses are braced for the risk of further flash floods and crippling clean up costs as weather forecasters warn of more heavy rain.
Cork and Belfast bore the brunt of the first swathe of freak downpours as storm drains and gulleys proved useless against deluges over seven hours.
At the height of disruption more than 10,000 homes in the Cork area and 1,000 in Northern Ireland suffered blackouts.
Flood damage hit hundreds of homes and businesses in the affluent Cork suburb of Douglas with the village streets inundated by several feet of water, the shopping centre and well known local pubs and restaurants worst hit.
Local concerns centred on whether a storm culvert designed to cope with a major flooding incident was able to wash away the rain water.
Douglas had suffered the heaviest rain in the country in a short blast on Wednesday evening - 49.1mm.
Some of the other hardest hit areas included Clonakilty, where the Farla river was close to bursting its banks most of the day with the town cut off for hours, and Glanmire where some homes in one estate ended up in five feet of water.
Nearer the city, the southside suffered the most with homes in Greenmount, Bishopstown, the Viaduct, Turner's Cross, Ballyphehane and Togher badly damaged.
"The council is continually monitoring all wastewater and water service facilities to ensure continued service but at present all are operating as normal," a spokesman for Cork County Council said. "The council are also in contact with the ESB regarding power issues at pumping stations and routing emergency generating equipment."
Met Eireann said 50mm of rain fell in a three-hour period across Cork on to already saturated ground - three times the average June total has fallen in Cork this month.