Road closures are in place and some public transport services have been cancelled as heavy rain continues to fall across Northern Ireland.
The owners of flooded businesses in south Down are facing expensive clean-up operations after Newry’s canal burst its banks.
Flooding also caused disruption in other parts of counties Down, Antrim and Armagh.
The Met Office said continued flooding and transport disruption is likely.
Water levels in the most heavily affected areas have receded overnight, but poor weather is expected to continue with Storm Ciarán expected to move in later and continue on Thursday.
And any rain will fall on wet ground in south Down, making flooding more likely.
The railway line to Bangor has been closed due to flooding and train services to Londonderry have been stopping at Coleraine with rail replacement buses in place, operator Translink has said.
Passengers have also been warned of delays on the Portadown line.
Some business owners in Newry’s Sugar Island area said the floodwaters had caused thousands of pounds’ worth of damage.
Many businesses in the area have no flood insurance as they have previously been affected by floods, and some estimate that repairs could take months.
Solicitor Kevin Neary said the basement of his premises was under several feet of water.
“It’s the same as what happened in 2007 when we were similarly flooded,” he told Good Morning Ulster on Wednesday morning.
“The consequence for a lot of businesses in Newry is that since 2007 they cannot get flood insurance.”
He added: “You’re effectively sunk, you’re having to bear the losses yourself which is where we’re all facing at the moment, 80-odd businesses.”
Paul McCartan, owner of McCartan Bros menswear store, said it would cost him around £250,000 to repair and restock his shop.
He said it was “gut-wrenching” as “there are people dependent on me”.
“But we’ll fight through this and we’ll get through it,” he added.
The BBC’s reporter Cormac Campbell, in Newry, said the county Armagh side of the city was bearing the brunt, while businesses in county Down were still open and roads were passable on Wednesday morning.
The Department for Infrastructure said more than 800 calls had been made to its flood incident line and more than 12,000 sandbags had been used.
They urged the public to stay away from flooded areas.
Is climate change to blame for the flooding in Newry and Armagh?
You can’t point at one single event and say: “That’s climate change”. It’s a cumulative thing.
But that’s where the 150 years of meteorological records we have on the island of Ireland come in, which scientists at the Icarus Climate Research Centre in Maynooth have analysed.
And their findings are unequivocal – the signals of climate change are clear all over the island.
Not only have temperatures risen here in line with global changes, they have brought with them more rainfall and that rainfall is more intense.
So we are now in a situation where it is all about adaptation and mitigation – planning for something we have not dealt with before while trying to reduce our impact on the planet long-term.
There are worries that the worst is yet to come, with “unprecedented” water levels disrupting crews dealing with the flooding.
“We have measurements on the rivers, loughs, tides and we haven’t seen this before,” Paddy Lavery from the Department for Infrastructure said.
More rainfall forecast for the rest of the week would be affecting already “very saturated ground”, he added.
“This is an area we haven’t dealt with. We have a finite resource. Where is the water to get away to?
“We are resorting to providing sandbags to protect properties,” he said.
Killowen, on the northern shore of Carlingford Lough, had more than a month’s rain in 48 hours. Between 9am on Monday and 9am on Wednesday the weather station there recorded 110.4mm of rain. The average for the month of October is 100.47mm.
Meanwhile in the Republic of Ireland, a status yellow warning for rain has been issued for counties Cork, Waterford, Carlow, Kilkenny, Wexford and Wicklow.
Irish forecaster Met Éireann has warned of possible flooding in places as heavy rain falls on already saturated ground.
The warning takes effect from 19.00 local time on Wednesday until 07.00 on Thursday.
A status yellow rain warning is in place in County Kerry until 12:00 on Wednesday, while a separate yellow wind warning is in effect for counties Kerry, Clare and Galway from 05:00 local time on Wednesday until 11:00.
Strong and gusty westerly winds and frequent bursts of heavy rain are expected.
The stormy weather follows flooding in several parts of the country earlier this week, with homes and businesses in parts of County Louth and Wexford among the worst hit.