National weather agency AEMET said its highest red alert would be in effect from 10:00 am (0800 GMT) on Friday in the eastern coastal province of Alicante, as well as in the neighbouring region of Murcia.
"Extraordinary danger. Flooding and flash floods may occur. Follow the advice of civil protection," the agency wrote on X.
Rainfall totals could exceed 140 millimetres (five and a half inches) in 12 hours, especially in Valencia, the weather office said.
In Murcia, authorities announced the region's universities and schools in more than 10 municipalities would remain closed on Friday.
Regional authorities in Valencia sent a telephone alert to Alicante residents urging the utmost caution as firefighters in the province reported around 100 rain-related incidents.
Flights to Alicante airport were severely delayed or diverted, according to operator Aena, while national railway company Renfe offered free ticket exchanges and cancellations on some routes as passengers were discouraged from travelling.
Widespread flooding in another part of Valencia in October 2024 killed more than 200 people, Spain's worst such disaster in decades.
The catastrophe sparked public fury over warning systems and the emergency response. Residents continue to protest, accusing officials of having failed to provide timely alerts.
Heavy rains lashed the region last month, forcing the closure of schools and universities, disrupting rail and road travel and causing localised flooding.
Because a hotter atmosphere holds more water that evaporates from a rapidly warming Mediterranean Sea, climate change increases the risk and intensity of flooding from extreme rainfall in the region.
mig-ds/imm/gv
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