Two bodies - 55 km apart - were fished out from the Ganga canal in western Uttar Pradesh's Muzaffarnagar during a desilting process.
Desilting is the removal of fine silt and sediment that has collected in a river, or a water body, to restore its natural capacity.
The bodies have been identified and the families informed. A probe is underway, the police said.
Dilshad Ansari, 27, who had been missing since January, was found in the backseat of the car, which sources say was borrowed from a friend. The man, a resident of the Baghra area in Muzaffarnagar, was identified through his driving license.
Mr. Ansari's brother, Wajid Ansari, had filed a complaint earlier this year at the New Mandi police station soon after his brother went missing.
The second body, of Harendra Dutt Atre, was found in the Sikheda area, 55 km away, from the spot where Mr. Ansari's body was found.
Mr. Atre had been missing since February.
"The family has been informed after identifying the body. Further investigation is being conducted and action will be taken accordingly," said Deputy Superintendent of Police.