There was a Met Office yellow weather warning in place in the area on Saturday evening.
The Met Office has also issued a fresh yellow weather warning for rain applying across Northern Ireland from noon to 9pm on Sunday.
The Northern Ireland Fire and Rescue Service said it received 106 emergency calls related to flooding between 7pm on Saturday to 1.30am on Sunday.
Firefighters responded to 49 incidents.
One person was rescued from a vehicle in water, and five people were rescued after becoming trapped within flooded properties.
Donegal County Council reported that heavy rain in East Inishowen has resulted in damage to roads and bridges in the area.
It warned of significant debris on the main Muff to Moville road, and on Sunday morning asked the public to avoid journeys in the area.
On Sunday police in Northern Ireland urged motorists to exercise extreme caution on the roads in Derry and Strabane, adding a number of routes are flooded and impassable.
DUP Foyle MLA Gary Middleton said the heavy rain has had a “devastating impact” on many properties across the area.
He said several businesses have been damaged by flooding in the Eglinton area.
On Saturday evening, the Western Health Trust said the Altnagelvin Hospital in Derry had to temporarily close some sections of the emergency department, while events at the Foyle Maritime Festival on Saturday evening were closed for the health and safety of visitors and staff.