Bridge Street in Newry has been badly affected, with cars under water
The worst flooding was in Counties Armagh and Down, particularly Newry.
Several homes and shops were evacuated on Bridge Street, Newry, on Thursday afternoon because part of the street was under two to three feet of water.
On Friday evening, some roads were closed in parts of County Armagh, including in Portadown and Loughgall.
Earlier, Trafficwatch NI advised staff in Greenbank industrial estate in Newry to leave before a high tide at 16:00 GMT.
Further problems on Friday meant Bridge Street and several other roads across Northern Ireland were closed, although many have now reopened.
Newry businessman, Shealan Strain, who owns The Gentry clothes store on Bridge Street, said he tried to protect his shop with sandbags on Thursday afternoon but had to evacuate because of the volume of water.
"Within about 20 minutes it was coming in the front and the back, so basically, we just had to leave," he told BBC Radio Ulster.
Mr Strain said when the water subsided at about 20:00 GMT, he returned to the shop and spent almost four hours cleaning up the damage.
'Already saturated'
However, he said has been told the street flooded again on Friday morning.
"So what do we do now? I haven't had one phone call from the council informing me of what has happened, what the plan is and if there is any chance of flooding again," Mr Strain told the BBC.
A bridal shop next door was also flooded, and it led to problems for one bride who is getting married on Friday.
Caroline Bramwell was due to pick up her wedding dress from the shop on Thursday afternoon, but was told it was inaccessible due to the floods.
However, local police officers came to the rescue, wading through the shop to retrieve Ms Bramwell's dress.
Part of Newry's Bridge Street was under two to three feet of water at one stage on Thursday evening
They have been based there while their own offices in Adelaide Street were being refurbished.
A DEL spokesman said they had re-located back to the Adelaide Street premises on Friday because the flooding had caused a power failure, but hoped to be back in Clarence Court on Monday.
He added that services had not been affected.
Staff in the Department for Regional Development who shared an office with DEL in Clarence Court have also had to leave the premises.
The rain has been accompanied by strong winds, as seen in Whitehead County Antrim
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