Many victims were elderly people who were asleep in the town of Krymsk when the storm broke in the agricultural region of Krasnodar overnight.
The flooding damaged thousands of homes, blocked railways and roads, and halted oil and grain shipments from the Black Sea port of Novorossiisk.
A car lies submerged in a flooded street in the village of Novoukrainsk, near the southern Russian town of Krymsk, July 7, 2012.
"There are lots of overturned cars, even huge trucks. Brick walls have been washed away," said Vladimir Anosov, a resident of the village of Novoukrainsky near Krymsk, a town surrounded by mountains about 300 km (190 miles) northwest of Sochi where Russia will host the 2014 Winter Olympics.
"People are on the street, they are at a loss what to do. Helicopters are flying overhead, they are evacuating people from the flooded areas. The floods are really, really huge," he said by telephone.
Russian news agencies said President Vladimir Putin was expected to visit the region to inspect the damage and meet residents, some of whom criticised the rescue operations.
It was not immediately clear what the impact might be on the grain harvest, an important part of the regional and national economy.
"We found several streets with corpses covered in canvas. People there are in shock. They keep on mumbling that they had not been warned ... There are lots of Emergencies Ministry staff, but they are struggling to cope with the disaster," a reporter on Krasnodar's 9 TV channel said.
Police put the death toll in the Krymsk area alone at 92 and said two had been killed in Novorossiisk and nine in Gelendzhik.
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