A Met Office alert issued for Antrim, Armagh, and Down on Friday was due to end at noon but the clearance of the rain has been slower than anticipated.
The warning area has also widened on Sunday to include parts of counties Londonderry and Tyrone.
The Met Office is expecting a further 10-20mm of rain in places, on top of what has already fallen, before clearing from the southwest later on Sunday afternoon.
Met Office forecast up to 30mm of rain in the affected areas, with up to 100mm of rain possible over the Mourne Mountains.