Images on state media showed water gushing down the steep roads of mountainous Ha Giang province, a popular spot for motorcycle tours, with vehicles overturned and abandoned in the floodwater.
Residents in Ha Giang city stood on rooftops waiting for rescue.
Around 400 foreign tourists were evacuated from the flooded area.
It has been raining heavily and continuously in the province since Saturday. Thousands of homes have been partially submerged and many roads damaged, state media said.
High water on the Lo river had triggered "floods and landslides", according to a statement on the website of the provincial authorities.
Access to three communes bordering China had been cut off due to landslides, the statement said.
Three people died after being swept away in floodwater or buried in landslides, according to state-run Voice of Vietnam.
Serious flooding was also reported over the weekend in the northern port city of Hai Phong and Quang Ninh province where UNESCO World Heritage site Ha Long Bay is located.
Vietnam is frequently lashed by harsh weather in the rainy season between June and November.
Last year, natural disasters including floods and landslides left 169 people dead or missing in the Southeast Asian nation.
Scientists have warned that extreme weather events globally are becoming more intense and frequent due to climate change.
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