The Fire and Rescue Service responded to almost 400 emergency calls in a short period as homes and several roads were flooded.
Residents are now counting the cost of damage caused by the flooding.
East Belfast was particularly affected by the downpour. Connswater Shopping Centre had to close after water poured through ceiling vents.
Strandtown Primary School and police station were also flooded.
Other areas affected were Magherafelt, Lisburn, Omagh, Cookstown and Dungannon.
The Fire and Rescue Service has advised anyone with water in their premises to turn off the electricity at the mains.
A spokesperson for Connswater Shopping Centre said no serious damage was caused. The centre has since reopened.
About 80 residents at Towell House old people's home on the King's Road in east Belfast had to vacate the building after it was badly damaged by flood water.
Ladas Drive, which had been impassable, has reopened, as has Montgomery Road and Alexander Road.
Meanwhile, rainwater leaked into the third and fourth floors of Parliament Buildings at Stormont.
Deputy Speaker John Dallat told MLAs the flooding may have damaged the building's fire alarm system causing it to be activated by accident.
Floating cars
It was also reported that cars were seen floating down Ladas Drive and Channing Street, off the Castlereagh Road.
The Ormeau Road, Annadale Embankment, the Newtownards Road, the Ravenhill Road and the Somerton Road in the north of the city were also affected.
Regional Development Minister Conor Murphy said he hoped lessons could be learned.
"The infrastructure needs a significant investment, but I will be looking for reports from the Water Service and the Road Service as to what issues were out there, where things can be dealt with better and what improvements can be made."
South Belfast MP Alasdair McDonnell said an emergency flooding taskforce should be set up to deal with such situations.
"A cross departmental and multi-agency approach is required to ensure proper planning and a swift joined-up response in the event of emergencies," the SDLP representative said.
Outside Belfast, the Knockmore Campus of Lisburn Institute had to close after the building became waterlogged.
All classes at the institute have been suspended for the remainder of the week.
Heavy flooding also caused major congestion on the roads around Omagh.
A branch of Dunnes Stores in the town had to be evacuated after the building became flooded.
Earlier, Met Office forecasters predicted a period of exceptionally heavy and prolonged rainfall later this week.
Many places will see further rain but the worst affected areas are likely to be Northern Ireland and northern parts of England, where rainfall totals over a few days may be close to the monthly average for June.
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