Authorities declared a curfew in Volos, a city of nearly 140,000 people, as a storm named Elias made landfall, swiftly turning streets into rivers.
The storm had earlier caused flooding in the island of Evia near Athens.
Villages outside Volos have also been evacuated.
Earlier in September central Greece was devastated by cataclysmic amounts of rain dumped by Storm Daniel, destroying crops and killing tens of thousands of farm animals across a wide area that is the heart of Greece's agricultural production.
Agriculture Minister Lefteris Avgenakis on Wednesday said clean-up crews had disposed of over 180,000 dead livestock and poultry, but were still unable to reach over a dozen chicken farms cut off from access roads.
Destroyed crops include cotton, corn, wheat, apples and kiwis, he said.
Facing a barrage of criticism at a perceived failure in cooperation between the army and civil protection in the hours following the disaster, the government has pledged over two billion euros ($2.1 billion) in reconstruction funds.
EU Agriculture Commissioner Janusz Wojciechowski is scheduled to tour the central region of Thessaly on October 5, Avgenakis said Wednesday.
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