The Spanish city of Benidorm and island Majorca are expected to be part of the hardest hit locations.
There is expected to be massive hail and thunderstorms along with winds that reach up to speeds of 60 mph on the coast.
Forecasters have issued orange and red notices for these areas.
The new storm comes only days after Hurricane Leslie killed 13 people when it smashed into the continent.
In other cities, such as Alicante, police have taken up extra patrols and have warned people on holiday to prepare for “severe weather conditions”.
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According to forecasters on the Costa Blanca, the mainland will be hit with heavy rain today.
Heavy rain is believed to reach Alicante between Thursday and Saturday with the strongest rains coming on Saturday according to the State Meteorological Agency.
Meteorologists are also expecting the Balearic Islands to be severely hit and have issued warnings for Majorca, Ibiza and Menorca.
Met Office forecaster Greg Dewhurst warned anyone going on holiday to check the local forecasts before they leave.
Mr Dewhurst said: “There will be heavy rainfall – between 200-400mm falling in the Balearics and also Catalonia, Valencia and Andalusia – and there is a risk of flash flooding in those regions.
“There will also be thunder and hail storms and gusty winds, with the storm beginning today, with the storm continuing tomorrow and into Saturday.
“The worst of the weather will hit Spain over the next 24 hours, with the weather beginning to settle by Sunday.”
Majorca was devastated by an “avalanche of water” last Tuesday that left several people dead including two Britons.
On Sunday night, the Aude area in southern France received several months of rain in the span of a few hours.
Hurricane Leslie left hundreds of thousands of people in Portugal stranded without any power and left dozens of people dead.
The wind reached speeds of 125 mph and threw trees onto cars throughout the capital Lisbon and the tourist city Porto.
Multiple flights to and from Lisbon were cancelled due to the extreme weather.