Police received around 100 phone calls on Sunday shortly after 11pm by residents reporting flooded cellars, garages and elevator shafts, Chur police said in a statement.
Three cars were stuck in underpasses as roads flooded, they said.
Some 40 units were mobilized to deal with the clean-up, which lasted until the early hours of the morning.
No one was harmed.
The cost of the flooding cannot yet be estimated, police said.
More rain and isolated storms are forecast for Chur and other parts of eastern Switzerland on Monday, said Meteo Suisse.