More heavy rainfall is forecast for Tuesday as Storm Francis moves eastwards across Ireland.
Rain overnight and on Tuesday morning caused flooding in some areas with AA Roadwatch urging drivers to be careful during the wet and windy conditions.
Flooding was reported in Freshford, Co Kilkenny and on the N85 near Ennis, Co Clare.
In Kerry, flooding was reported on the N70 in Cahersiveen but the N71 is has been deemed passable with care between Kenmare and Bonane Village at Dromanassig.
Emergency services in Co Sligo were working to remove a fallen tree on the N16 near Glencar.
Parts of Cork experienced flooding for a second week in a row as a result of the heavy rain, but not to the same extent as during Storm Ellen.
John Donegan, senior engineer with Cork County Council, said up to 50 homes and businesses in Bantry were damage as a result of the overnight rain.
Local authority crews were working to clear any damage caused when a drainage system could not cope with up to 25mm of rain that fell in a two hour period, he told RTÉ radio's Morning Ireland.
New Street, Main Street, Barrack Street and the Square in Bantry were the worst affected with council crews and the local fire brigade working with residents and business owners to clear debris and pump away remaining flood water.
Mr Donegan said high tides would not be a concern this week as they were last week, but a yellow wind warning remains in place.
Measures implemented in Skibbereen after flooding during Storm Ellen last week held and no issues were reported there, Mr Donegan said.
“We’ve been very unlucky that the rain has been so intense and localised,” he added.
Met Éireann meteorologist Linda Hughes told Morning Ireland that the worst of the storm had passed in the southwest, but warned that the northern half of the country would see heavy rainfall until 6pm. This could cause flash flooding in Connacht and Ulster, she said, and further issues could occur in parts of Munster as rainfall runs down from higher ground.
A status orange rainfall warning remains in place for all of Connacht, along with Cork, Kerry, Wexford, Waterford, Cavan, Monaghan, and Donegal until 6pm. A status yellow rainfall warning is in place for counties Dublin, Carlow, Kildare, Kilkenny, Laois, Longford, Louth, Wicklow, Offaly, Westmeath, Meath, Clare, Limerick and Tipperary until 9pm.
A status yellow wind warning for Munster, Dublin, Carlow, Kilkenny, Wexford and Wicklow is also in effect and will expire at 7pm on Tuesday.
Very windy or stormy conditions are expected, with southwest winds veering westerly, reaching mean speeds of 55km/h to 65km/h, with gusts of up to 110km/h possible.
Ms Hughes warned that the strong winds could result in trees falling over throughout the day and advised motorists to take extreme caution.
The persistent rain will become mainly confined to Ulster by the evening. Highest temperatures of 17 degrees have been forecast for the day.
Heavy rainfall in August was not unprecedented, said Ms Hughes, as conditions were influenced by the hurricane season.