The weather alert is in place from midnight tonight until 7pm on Tuesday as "persistent and occasionally heavy bands of rain" will hit on Sunday night and last right through through to Tuesday evening.
Forecasters warned of a risk of "localised spot flooding with a heightened risk of flash flooding in mountainous regions where accumulations are expected to be highest."
And the warning will be reviewed and could be elevated to a higher level of threat, Met Eireann warned.
Meanwhile, a weather warning has also been issued for five counties in Northern Ireland also as forecasters warn of "persistent heavy" rain ahead tomorrow.
The UK Met Office have placed Armagh, Down, Fermanagh, Tyrone and Derry under a Status Yellow warning while Met Eireann have issued a four-day weather advisory for the entire country, with warnings to follow.
And the entire week looks set to be a washout with a weather advisory in place from midnight and lasting until 6pm on Thursday.
A forecaster cautioned: "Conditions turning unsettled by the end of the weekend, with a spell of very wet and at times windy weather on Monday and Tuesday.
"Persistent and locally heavy rainfall, coupled with high soil saturation levels, brings a risk of river and surface flooding.
"Unusually high tides combined with strong winds gives an elevated risk of coastal flooding. Warnings will be issued on Sunday."
Meanwhile, the Northern Ireland weather warning reveals that heavy rain may cause disruption to transport and flooding.
It comes into effect at 5am on Monday morning and will last until 3am on Tuesday.
Today, however, will be mostly dry with only a few isolated showers in the east and northeast.
But patchy rain will creep in during the evening ahead of a deluge on Monday.
A Met Eireann forecaster revealed: "Any lingering fog will clear this morning to give a mostly dry day with sunny spells and just isolated showers mostly in the east and northeast.
"It will remain cloudier over Munster however, with patchy rain and drizzle at times. Cloud will spread over all but the northeast of the country through by evening with patchy rain, becoming more persistent later, especially in the west and north. Highest temperatures of 12 to 15 degrees in light to moderate south to southeast breezes."
An area of low pressure will dominating for the week, bringing spells of wet and sometimes windy weather.