The heavy rains have mainly affected the southern provinces of Alicante and Almeria which have been hit by several thunderstorms since the weekend.
Torrential rains have also lashed Madrid, where several roads were cut on Monday night due to flooding.
Flooding also temporarily interrupted traffic along stretches of three of the Spanish capital's 12 metro lines, local officials said.
State weather agency AEMET placed most of northern Spain on on alert Tuesday due to the risk of thunderstorms, hail and strong winds.
Most of the eastern region of Valencia, which is home to important tourism resorts such as Benidorm, were also on alert, along with parts of central Spain.
Experts said the torrential rains -- which tend to trickle off instead of seeping into the ground -- were insufficient to end the deficit in Spain's water reservoirs.
Spain's reservoirs, which store rainwater for use in drier months, were at just 47.5 percent of their capacity during the final week of May, down slightly from 47.7 percent during the previous week, according to environment ministry figures.
That is well below the ten-year average of around 68 percent.
Spain has registered the driest start to a year since records began, with less than half the average rainfall during the first four months of 2023, according to AEMET.
The government earlier this month approved measures worth more than two billion euros to alleviate the impact of the prolonged drought, especially on the agricultural sector.
Spain is the European Union's biggest producer of fruit and vegetables, and the world's biggest exporter of olives.
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