Police said the body of Gohouri, who won 13 caps for Ivory Coast, had been found in the river at Krefeld near Duesseldorf, German sports news agency SID reported.
Police said an autopsy found no signs of violence. They gave no indication as to other possible causes of death.
Gohouri, 34, had told his teammates he was heading to Paris to see his family but the former Wigan and Borussia Mönchengladbach defender never arrived.
His family travelled from France to Germany to report his disappearance.
Gohouri, who started his career at Paris Saint Germain but failed to make the first team, vanished after attending German fourth tier club TSV Steinbach's Christmas party on December 12.
Steinbach coach Thomas Brdaric noted after Gohouri went missing that "there is much speculation -- but I hope it is not true -- that he has personal problems and has abandoned his responsibilities."