The body of Cafe Coffee Day founder V.G.Siddhartha has been identified, police Commissioner Sandeep Patel said. He didn't give other details.
An autopsy was being conducted and the cause of death was not disclosed.
Siddhartha, 60, had left Bangalore on Monday and left his car near a bridge in Dakshina Kannada district in Karnataka state.
He told his driver to wait, saying he was going for a walk near the bridge. When he didn't return for two hours, the driver notified police, police officer Sasikant Senthil said.
"I saw a body floating while I was fishing and then I informed the police. I participated in the rescue operation," the New Delhi Television news channel quoted Rithesh, a fisherman, as saying. Rithesh uses one name.
He leaves behind a coffee shop chain with more than 1,500 stores across India with revenue of $630 million in 2017-18.
It also has outlets in Austria, Czech Republic and Malaysia, according to the chain's website.
Police were investigating a letter that appeared on social media in which Siddhartha alleged he was facing harassment from tax authorities that caused a serious liquidity crunch.
The letter purportedly written by him also said that he failed to create the right profitable business model despite his best efforts and was facing pressure after borrowing a large sum of money from a friend to buy back shares.
Siddhartha is survived by his wife and two sons.
He was a son-in-law of S.M. Krishna, a governing Bharatiya Janata Party leader and a former External Affairs Minister (2009-2012) and Karnataka's top elected official (1999-2004).