Weather forecasters warned the relief would be short-lived because another storm was expected to pour heavy rain on already saturated ground on Saturday.
Portugal had barely recovered from last week's battering by rain and winds that killed five people, injured hundreds and left tens of thousands without power.
This week's Storm Leonardo has left one dead in Portugal and lashed the southern Spanish region of Andalusia, where rescuers were searching for a missing woman and evacuated 8,000 people.
Scientists say human-driven climate change is increasing the length, intensity and frequency of extreme weather events such as the floods and heatwaves that have struck both countries in recent years.
Spanish Prime Minister Pedro Sanchez was due to visit the hardest-hit areas of Andalusia on Friday, his office said without providing further details.
After some municipalities received several months' worth of rain in 24 hours, Spain's AEMET weather agency lifted its second-highest orange alert for storms in Andalusia but warned of the impending Storm Marta.
"On top of what has already accumulated in previous days, it is highly likely to trigger further floods, spates and landslides" in mountainous parts of Andalusia, AEMET spokesman Ruben del Campo said in an audio note.
Portugal's IPMA weather agency said Marta would "contribute to another rise in river flows", notably in the south and the Lisbon region.
On Friday, attention turned to Portugal's northern Douro river which burst its banks outside the city of Porto overnight without causing victims or evacuations.
"As long as the flows remain high, we will maintain the red alert for the Douro," the captain of Porto's port, Pedro Cervaens, told local media.
"The water has reached the terraces" of cafes, but "no major damage has been reported for now", he said.
Authorities evacuated around 600 people on Thursday, with a spate of the Tagus river in central Portugal triggering the highest flood alert.
Prime Minister Luis Montenegro said "a devastating crisis" had hit Portugal, but the floods were not expected to delay Sunday's presidential run-off, despite a postponement request from the far-right candidate.
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