A new 'yellow' alert affects counties Armagh and Down overnight on Thursday, until 8am on Friday morning.
"Outbreaks of rain will become persistent and heavy overnight and into the early part of Friday morning," says the Met Office.
"With ground conditions becoming more saturated again, there is a risk of localised flooding. Drivers should be aware of some difficult driving conditions due to standing water and spray."
Ulster Unionist Jo-Anne Dobson said last week that part of the Upper Bann constituency had effectively become an extension of Lough Neagh.
The MLA said some homes and businesses in The Birches area of Portadown had been underwater for three or four weeks.
The Met Office Chief Forecaster said: "An active frontal system will cross Northern Ireland on Thursday night, bringing a spell of rain to all parts.
"The rain will be heaviest over South Down especially over high ground facing the strong to gale force south to southeasterly winds. Here, 20-30mm will fall quite widely with over 40mm possible in the Mountains of Mourne. The rain will clear to the east by daybreak on Friday."