In pictures: Floods in Northern Ireland and Republic of Ireland
About 20 houses in Magherafelt, County Londonderry, were flooded on Tuesday night.
The Fire and Rescue Service said it received 33 calls in the Magherafelt area in the six hours until midnight.
In Omagh, County Tyrone, heavy rain also caused several streets to flood.
Cars drive through the rain-filled streets of Omagh on Tuesday evening. The town was one of the worst affected places following the torrential rain.
The heavy rain caused flooding on several roads in Omagh. Environment Minister Mark H Durkan said he had now activated the emergency payment scheme and individual households would be eligible for a £1,000 payment.
Letterkenny General Hospital was closed on Tuesday evening after "torrential rain" affected the hospital's Accident and Emergency department.
On Tuesday night, the hospital's car park and grounds were flooded as firefighters worked to pump water away from outside the building.