Pictures on state media showed residents navigating flooded streets in boats, while homes and cars were partially submerged.
"The city is flooded everywhere, with waters rising very quickly since Tuesday night," Hue resident Vu An told AFP, adding that power had been cut off in the city.
Heavy rain has pounded several provinces along the coast since Monday.
More than 2,000 people have evacuated their homes in central Quang Tri province, where three people are missing, authorities said Wednesday.
Some parts of the national highway linking north and south Vietnam have also been blocked by landslides due to the flooding.
Vietnam is frequently lashed by harsh weather in the rainy season between June and November.
Forecasters said water levels may remain high for the next two days before improving this weekend.
According to official figures, natural disasters including floods and landslides have left 136 people dead and missing in Vietnam this year.
Scientists have warned that extreme weather events globally are becoming more intense and frequent due to climate change.
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