South Down is expected to receive the most rain overnight, with 15-25mm of rain falling in a relatively short period, and areas of higher ground could see 40-50mm of rain.
This warning follows severe flooding in Downpatrick, Newry, and Portadown earlier in the month. The Shadow Secretary of State for Northern Ireland, Hillary Benn, visited affected businesses and expressed the devastating impact of the floods.
Many business owners felt blindsided by the flooding and highlighted the need for a flood warning system that can notify people in advance.
The UK government has pledged £15 million to help flood-hit firms in Northern Ireland cover cleanup costs and resume trading.
However, some have criticized the amount as insufficient, with calls for more financial support, especially in the run-up to Christmas. Hillary Benn plans to raise the issue of flooding and its response in Northern Ireland in Westminster next week.