Road closures are in place in counties Armagh and Down as heavy rain continues to fall across Northern Ireland.
A yellow weather warning for heavy rain is in place until 09:00 GMT on Wednesday morning.
The Met Office said continued flooding and transport disruption is likely, with 15-20mm of rain expected.
It comes after several businesses suffered extensive damage in the centre of Newry as the city’s canal burst its banks.
Flooding also caused disruption in other parts of counties Down, Antrim and Armagh.
The poor weather is expected to continue, with Storm Ciarán expected to move in later and continue on Thursday.
On Tuesday, the Department for Infrastructure said more than 600 calls had been made to its flood incident line.
Some business owners in Newry’s Sugar Island said the floodwaters had caused thousands of pounds’ worth of damage.
Many businesses in the area have no flood insurance as they cannot get cover for flood damage, with some estimating that repairs could take months.
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.
On Tuesday, some roads in other parts of counties Down and Armagh, such as Killowen, Moira, Ballynahinch and Bangor, were impassable.
Train services between Portadown and Dundalk were disrupted after the lines were flooded.
In Camlough, County Armagh, residents spent Tuesday surveying the damage caused to homes and businesses after flooding in the area.
Motorists were forced to abandon their cars as surface water closed the village’s main street.
In Newcastle, residents in Marguerite Avenue were placing sandbags at their front doors in an attempt to keep flood waters at bay.
Meanwhile in the Republic of Ireland, a status yellow warning for wind has been issued for counties Kerry, Clare and Galway.
Met Éireann has said strong and gusty westerly winds, as well as frequent bursts of heavy rain are expected.
The warning is in place from 05:00 local time on Wednesday until 11:00.
A separate status yellow warning for rain is in place for County Kerry until 12:00 on Wednesday.