Some 12,000 sandbags have been deployed as areas in the east of Northern Ireland have been hit with flooding.
An estimated 80 businesses in Newry are counting the cost after the city’s canal burst its banks on Monday night, submerging sections under water.
Further rain is expected with the arrival of Storm Ciaran later on Thursday.
A Department of Infrastructure official said they still have concerns about Newry, over the impact of high tide potentially causing further breaches of the canal wall.
Gary Quinn from the Rivers Agency said they have placed a large number of sandbags in the city.
“We have a focus on Portadown, we have a focus on Banbridge. The Bann river level is rising, but there are numerous towns and villages where we have had to respond to some more local type impacts,” he told the BBC.
“But our main focus is on Newry and Portadown.”
Roads and some train services have been disrupted in counties Down, Antrim and Armagh amid rising waters.
On Wednesday morning, public transport authority Translink said the Bangor train line was closed for a period. It has since reopened.
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 lough levels continue to be monitored as levels rise and will continue be monitored over the coming days.
“People are urged to stay away from flood defences, flooded areas and watercourses,” they added.
The Met Office has issued a yellow warning for rain for the eastern half of Northern Ireland on Thursday.