A yellow 'Be Aware' warning is in place until midnight for Northern Ireland and winds of up to 70mph are expected to hit the east coast.
The Met Office advised: "The rain will be accompanied by gales and possibly severe gales for a time across Scotland and Northern Ireland in particular.
"The public should remain aware of the potential for further localised disruption due to heavy rain and/or the very strong winds."
In Broughshane, a small village near Ballymena, a river burst its banks and flood waters rose up towards nearby houses.
Michael Meharg, a local farmer, was unable to reach his cattle due to the flood waters.
"I think any farmer in Northern Ireland with stock near rivers would have been concerned last night because of the unprecedented amount of rain," he said.
"The floods that have come here in Ballymena where I farm with traditional cattle.. are particularly high, but the Met office did warn us that there were floods coming, the amber warnings were out.
"As a result of that, I was able to move cattle two days in advance, now unfortunately there was a lot more rain than expected , I think there has been up to four inches of rain in places and some cattle are up to their knees in the water.
"I spent a bit of a sleepless night last night again, as I'm sure many farmers across Northern Ireland did, worrying about our stock," he added.
Luckily, Mr Meharg's cattle were fine despite the bad weather conditions.
I spent sometime with elderly residents last night who were scared to go to bed in case their homes were going to flood.
Cllr Audrey Wales
Audrey Wales, a DUP councillor for the area, said over 300 sandbags had been delivered to try and keep water out of people's property.
"All the agencies were out last night delivering sandbags etc along with the community association in Broughshane and the angling club," she explained.
She said that a potential development site would add to the flooding problem and she has received over 200 objections to the plan from local residents.
"If something is built on this site it will push the water even further into the village and flood the village of Broughshane even more than you've witnessed today," she added.
Elsewhere, some areas of Great Britain are to experience a whole month's rainfall in just 24 hours, according to the experts.
England and Wales are preparing for flooding from rivers and surface water as up to 100mm, almost four inches, of rain could fall by the end of the day, the Met Office said.
Around 60 flood warnings have been issued in England.
Meanwhile, Met Éireann has a gale force wind warning in place for Tuesday.
Further heavy rain is expected to fall with a risk of local flooding especially in the east and north of the island.
There will be gales in places and some severe gusts between the northwest and northeast direction throughout the day and night on all Irish Coastal Waters and on the Irish Sea.
On Monday, the region was battered by persistent heavy rain and high winds - particularly on the east coast.
Northern Ireland was on an amber alert from 3pm onwards on Monday - but from early morning, the weather wreaked havoc for motorists.
Co Antrim was thought to be worst affected by localised flooding and surface water.