City Hall instructed residents to stay inside and told commuters to avoid the city.
Homes and stores were flooded, roads were cut off, and train, bus and subway services were disrupted. Several schools canceled classes, and some tourist landmarks shut their doors.
Lisbon has long been prone to flooding. It stands at the mouth of the Tagus, the peninsula’s longest river, where it meets the Atlantic. Part of the city is built on two tributaries that feed into the Tagus.
Lisbon Mayor Carlos Moedas said extreme weather events are becoming more frequent due to climate change.
He said work will begin soon on two drainage tunnels which are expected to ease flooding.
The storm moved across the border into Spain later Tuesday, where heavy rain also flooded roads and houses.