The Co Down town's main shopping area - Market Street - was the worst affected.
The owner of a dry cleaning business said it had been the eighth time in the past 10 years that the shop had flooded.
Another businessman, Bartley Murphy of Murphy's Bar, said he arrived to find 2 ft (60 cm) of water in the building.
"It is horrendous. The sewage is on the floor now," he said.
He told BBC Radio Ulster's Nolan Show: "This happens twice a year. Where is the contingency plan? I have phoned the water board, the police and environmental health. Where are they?"
"The Department of Environment should be here helping the traders. There is a dry cleaner's shop with wedding dresses... he has six inches of water in the shop."
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