A yellow alert was issued for the second day in a row by the met office on Wednesday.
It is in place from 10am until 4pm.
According to the warning, isolated heavy thunderstorms are likely to affect the area, and shower rates may exceed 35 mm per hour.
During the day the weather is forecast to be mostly cloudy. Rain and snow in the higher mountains are expected.
Temperatures will rise to 18C in most areas and 6C around Troodos.
At night, temperatures are expected to drop to 4C inland, 7C in coastal areas and -2 in the mountains.
More rain and thunderstorms are forecast for Thursday morning but gradually the weather will become clear and temperatures will rise.
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