The Met Office has put a yellow alert in place for the region from early afternoon until 8pm.
Northern areas are likely to be worst affected by the heavy, slow-moving, thundery showers.
The Chief Forecaster warns that those showers could bring more than 30mm of rainfall within just two or three hours - although they should clear later.
The public should be aware of the potential for localised flooding, with standing water and spray on roads also possible.
The Rivers Agency is also warning the public to be vigilant when it comes to flooding.
"We're as well prepared as possible - we've been checking infrastructure, making sure we have staff on call and also working with councils to make sure sandbags are available close to at risk areas," Philip Mehaffy from the agency told UTV.
"While the government agencies will do their absolute utmost to protect people from flooding, there are measures that property owners can take themselves."
Emergencies from Co Donegal have been diverted to A&E at Altnagelvin as Letterkenny General Hospital has been severely damaged in flash flooding.
Millions of euro worth of damage was caused to the building and its specialist equipment when heavy downpours pushed a torrent of water through the building.
A nearby stream had burst its banks, drains were overwhelmed and wards and corridor were engulfed in flood water contaminated with sewerage and debris.
"It was totally devastating," Mayor Pascal Blake told UTV. "The place is totally destroyed. It was hit like a Tsunami and it's left drastic results."
Hundreds of volunteers have been helping in the cleanup and the Western Trust say they will continue to provide support to their colleagues in Letterkenny, while emergency calls are being diverted Altnagelvin and Sligo Hospital in the meantime.
Parts of Co Down have been affected by heavy rain on Monday, with flood water reported in Banbridge and Downpatrick.
Similar weather conditions look likely throughout the week, with Tuesday starting bright but bringing heavy showers in the afternoon.
Flooding can be reported using the Flooding Incident Line on 0300 2000 100.
And if you've been taking pictures of the recent lightning or floods, you can add them to our Summer Storms gallery!
- Move cars, pets, food, valuables and important documents to safety
- Turn off gas, electricity and water supplies if it's safe to do so
- Try to stop water entering your home by using sandbags and floodboards
- Seal airbricks with plastic covers or cloths/towels
- Put plugs in sinks and baths and weigh them down
- If you don't have valves fitted which allow flow of water in one direction, you should plug water inlet pipes with towels or cloths and disconnect any equipment that uses water (washing machines, dishwashers, etc)
- Be prepared to evacuate your home