The flooding in Binh Thuan province was triggered by heavy rain and the discharge of water from an irrigation reservoir on Tuesday and Wednesday.
"We lost all our dragon fruit and cucumber crops this year," Ho Van Trung, 66, told AFP.
Vietnam dragon fruit exports generated a record $1.8 billion in 2018, but the figure has been declining in recent years.
Binh Thuan province is home to Vietnam's biggest growing area, measuring 28,000 hectares and producing 600,000 tonnes of fruit each year.
The fiery red and green fruit with a scaly skin that gives it its name thrives in hot and dry conditions, but, as part of the cactus family, cannot stand immersion in water.
On Thursday, farmers in two villages in Binh Thuan's Ham My commune said the floods in the area were "unprecedented".
"My house and my gardens growing dragon fruit and cucumber are all submerged," Trung said.
Living close by, Dao Thi Bich Thao and her husband had to evacuate their one-storey home after it flooded.
"Water came so quickly that we could only move our TV and refrigerator and then flee," Thao said.
Around 200 households and 400 hectares of crops, mostly dragon fruit, had been flooded, a local official in Ham My commune told state news site VNExpress.
More than 70 residents moved to higher ground as their homes were temporarily uninhabitable, the report said.
Scientists have warned that extreme weather events globally are becoming more intense and frequent due to climate change.
Other parts of Vietnam have also been hit by heavy rain and floods in recent months.
The country's north has suffered through an extremely wet summer, with mountainous areas in the northwest particularly badly hit since early July.
Across the country, nearly 29,000 houses have been damaged and 90,000 hectares of crops destroyed, Vietnam's General Statistic Office (GSO) said late last month.
Floods caused around $85 million in damage in the first seven months of the year, double that of last year, according to GSO.
Ninety-one people were killed or reported missing due to adverse weather during that period, it said.
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