A bypasser saw the roof of the small car floating in the river in the North Rhine-Westphalian city of Minden on Friday. Divers from the Bundeswehr recovered the car, which held the bodies of a 58-year-old man and a 44-year-old woman.
But the married couple did not die in the river, police said. The woman was found bound and gagged in the car trunk, while the man was in the driver's seat. An autopsy showed that the woman had been suffocated.
The evidence leads police to believe that the man killed his wife, put her in the trunk, and drove the car into the Weser River.
The couple had been living separately since 2007. The man was from the Lower Saxony city of Raddestorf.
A murder commission is investigating the case.