Rain warnings have been issued for nine counties, with Status Orange and Amber alerts on both sides of the border.
The Orange rain and thunderstorm warning issued by Met Éireann for counties Dublin, Louth, Wicklow and Meath came into effect at 12am and will last until 2pm.
The UK Met Office issued an Amber rain warning for counties Antrim, Armagh and Down. That warning will be in effect until 8am this morning.
Those counties are currently under a yellow rain warning until 6pm.
Met Éireann is warning that very heavy rainfall is expected.
It warned of widespread surface flooding, very difficult travelling conditions, lightning damage and very poor visibility.
The UK Met Office said some places in Northern Ireland are likely to have between 50 to 75mm of rain in a short space of time, with a risk of flash flooding.
There are reports of heavy rain in the Enniskillen area of Co Fermanagh with some roads flooded.
The PSNI is advising road users that the Marble Arch Road, Florencecourt and Sligo Road in Enniskillen are all impassable due to floods.
They said flooding is also affecting other parts of west Fermanagh.
"Please take care when travelling, slow down, and exercise caution on affected roads," the PSNI added.
Meanwhile, a Status Yellow rain warning issued for counties Kildare and Monaghan is in effect and will last until 2pm.
