An increase in waters levels led to the Ganges flowing above the danger mark at slightly above 71 metres at the weekend, pushing the water into low-lying urban areas and submerging the famous ghats and nearby houses, officials said.
People at some of the ghats — stone slab steps down embankments along the river bank — have moved makeshift crematoriums to higher ground after the water level submerged the river banks known for holding hundreds of cremations round-the-clock.
Authorities said more than 80 villages were submerged and 228 hectares of farmland on the banks of the holy river were flooded.
More than 2,600 people were moved to 16 flood relief camps set up by the state government, while 6,600 had moved of their own accord.
Kaushal Raj Sharma, district magistrate of Varanasi, said 4,000 households have moved their belongings to upper floors or other locations as the river's water level surged.
Mr Sharma said the administration had increased patrolling and monitoring of the river, with about 60 boats engaged in relief work.
Scores of medical teams have been sent to flood-hit areas with life-saving medicines and anti-venom kits.
Varanasi is one of the oldest inhabited cities in the world and is Hinduism's holiest site.
Millions of Hindus visit the city, particularly the banks of the Ganges, to practise religious rituals and seek salvation.
More than 1,100 people have died in India this year due to flooding and landslides, the government said last month.
At least 50 more were killed in northern Himalayan Himachal Pradesh and eastern Jharkhand and Odisha. More than 800,000 people were displaced from their homes in Odisha’s Balasore.
Torrential monsoon rain has this year been wreaking havoc in parts of the Indian subcontinent. More than 1,000 people have been killed in the extreme floods in Pakistan this month and millions of others displaced.