In Alcacer do Sal, emergency crews used boats to rescue residents after the Sado river burst its banks, cutting off parts of the town. Shops closed and the main avenue disappeared under water.
Portuguese civil protection said thousands of incidents were reported, from flooded homes to fallen trees, with hundreds evacuated. Soldiers were deployed to help rescue teams.
The storm has already killed one person in nearby Spain and follows weeks of severe weather across the Iberian Peninsula.
Forecasters warned the worst rain and wind could hit on 5 February overnight, while scientists say such extreme events are becoming more frequent as the climate warms.