In Dong An Vinh Village, farmer Le Van Chau said two of his six sao of onions had been submerged after days of heavy rain.
With just a week remaining before harvest, Chau feared the waterlogged crops could be lost unless they were pulled up immediately.
He said farmers were rushing to salvage as many onions as possible before prolonged flooding caused further damage.
The flooding has compounded difficulties for local growers already struggling with falling prices and weak demand.
According to Chau, onion prices have dropped to VND 20,000 (USD 0.76) per kilogramme, compared with the usual VND 40,000-55,000, a decline of around 36-50 per cent.
Under favourable conditions, each sao of onions can generate about VND 25 million (USD 950) in revenue. At current prices, however, farmers face difficulties recovering their substantial production costs.
Vo Tri Thoi, deputy head of Ly Son Special Zone's Economic Division, said heavy rain had caused localised flooding in residential areas and low-lying farmland.
Preliminary assessments showed that around two hectares of onion crops had been waterlogged, while strong runoff had eroded several fields.
Local authorities have been working with farmers to address the damage and salvage affected crops.
Thoi said early harvesting was considered the most practical way to minimise losses, particularly as onion prices remained low and weather conditions continued to be unpredictable.