Cleaning up is under way in Newry, Co Down as the full extent of the damage from serious flooding becomes apparent.
It is estimated that around 80 business premises have been affected by rain yesterday.
There had been fears that heavy overnight rain could exacerbate the flooding, which left much of Newry city centre under water after the city's canal overtopped its banks.
A 12-hour weather warning for rain had been in place across Northern Ireland from 9pm last night.
However the worst of the weather appears to have by-passed the south Down/north Louth area that suffered yesterday.
Concern remains about the impact of Storm Ciarán in the coming days and some 12,000 sandbags have been deployed across the country.
Newry's courthouse has been temporarily closed, with business moved to Craigavon.
The Department of Justice said the measure was to allow for remedial works to take place and to make sure the staff and public are kept safe.
"Court business will return to Newry Courthouse as soon as possible," they added.
Paul McCartan who owns a clothes business and who told RTÉ yesterday that he could not get flood insurance, today estimated that it could cost him £250,000 (€287,475) in lost stock and repairs.
which was hit with heavy rain yesterday
The water has receded in recent hours and people have begin to access buildings that have been under water for several days.
They include Riverside Reformed Presbyterian Church which ministers to around 40 people every week.
The church hall is still flooded and the church itself is now clear of water, but it had been flooded to a depth of several feet.
Sodden bibles were strewn around the church entrance and it will be months before they are able to have services there again.
"It's heartbreaking because it's a lovely building," Elder Noel McCune said.
"We've lent it to the community, various community groups over the past few years.
"There've been different plays and concerts here and everybody agrees it's a lovely building, a lovely church."
of the Kilkeel River which empties into the harbour
The damage was not just confined to Newry. South Down, south Armagh and north Louth were all badly affected.
A fishing boat in Kilkeel harbour was sunk by the swollen waters of the Kilkeel River which empties into the harbour.
It is now sitting on the bed of the harbour awaiting recovery.
Roads and some train services have been disrupted in counties Down, Antrim and Armagh amid rising waters.
This morning, public transport authority Translink said the Bangor train line will remain closed until further notice.
The Department for Infrastructure said it remained on high alert through the night.
It received almost 800 calls to its flooding incident line and has distributed more than 12,000 sandbags to the areas worst affected.
A spokesperson said river and lake levels continue to be monitored as they rise and will be over the coming days.
"People are urged to stay away from flood defences, flooded areas and watercourses," they added.
Further rain is expected with the arrival of Storm Ciarán this evening.
Eamonn Connolly, manager at Newry Business Improvement District, has said that this morning is "certainly better" as the water has somewhat receded even though water levels remain high, which is a risk.
He said that people are coming to terms with the damage that has been done and yesterday people were in shock, as parts of Newry were like a lake.
"We are deploying sand bags at an industrial scale, we have water pumps, we have water vacuums, we are relocating stock on the affected areas," he said.
Mr Connolly said it is only a certain part of Newry that was still closed and that the rest of Newry was open and trading.
He said that there is a fundamental issue where businesses have been excluded from insurance historically and many are now at risk with damaged premises and lost stock in the run up to Christmas and they will have to apply for government support because they will not bounce back otherwise.
He said they do not have a devolved administration at present so they are lobbying their local politicians and are pushing hard for support.
The Met Office has issued a yellow warning for rain for the eastern half of Northern Ireland tomorrow.
Frustration over financial support
Meanwhile, Sinn Féin MLA Conor Murphy has said that politicians are "fighting with their arms tied behind their backs" for financial support for businesses damaged in floods without a functioning Stormont.
Amid the ongoing collapse of the Stormont Assembly, senior civil servants are running government departments with restricted powers in the absence of ministers.
In terms of support, Mr Murphy said the household scheme is in place, but they are looking at what is available for businesses.
He said there was discussion between the departments on how to deal with this and they are awaiting the outcome.
"We want to make sure we press for as immediate a support as is possible for businesses that have suffered damage, and need to immediately get down to repair, restock and try and get businesses back open," he told reporters at Parliament Buildings, Stormont today.
"If Stormont was in place, I would have no doubt there would be several ministers in Newry yesterday and today assisting with the operation that is going on, but also turning their mind to collectively working together.
"We've done that in the past and unfortunately these types of severe weather instances are more and more frequent as global warming takes its toll.
"I have no doubt that we would be down with a number of ministers in the area trying to put their heads together and work up some support schemes to ensure that people get the level of support that they need.
"Whether that's happening in the near future or not, I don't know.
"I know we're up here today fighting with two arms tied behind our backs trying to get support for people, and clearly, the best situation would be if we had people in place in office to take decisions, that can put schemes in place, that can get out on the ground and try and respond quickly.
"That is a much more optimal situation than civil servants trying to figure these things out for themselves."
Additional reporting PA
