Hardy's cause of death has not yet been determined. He was 31 years old.
His body was found lodged in a dam in the river, according to the Fort Wayne Police Department.
According to multiple reports, Hardy's mother reported her son was missing on May 30.
Hardy, who was from Fort Wayne, played two seasons for the Bills (2008 and '09).
The Bills selected Hardy in the second round (41st overall) of the 2008 draft after the receiver compiled 191 receptions for 2,740 yards and 36 touchdowns at Indiana University.
The Bills sent their condolences to the Hardy family on Thursday.
Our support is with the Hardy family after the passing of former Bills WR James Hardy. pic.twitter.com/4ZgLDUwyPA— Buffalo Bills (@buffalobills) June 8, 2017
The 6-foot-6 Hardy also appeared in 23 games for Indiana's basketball team during the 2004-05 season. Indiana said Thursday in a tweet that it was saddened to learn about Hardy's death.
Bryan Payton, one of Hardy's teammates at Indiana, posted a poignant message and photo on Instagram of the two when they were high school rivals.
Payton called Hardy an "inspiration to me and many others."
Before James and I were ever teammates, we were opponents and competed in one of the most epic games of my career. I'll never forget presenting this picture to him and the laugh he gave! It's a pic from me leaping in front of him to make an interception in High School. He signed it for me before heading off to the NFL. In college, during our numerous rides together back to Fort Wayne, we would talk about our lives, families, goals, hopes, and dreams. And of course plenty of football. He believed in me and, in a way, gave me permission to be great at a time when I began to doubt myself. James was an inspiration to me and many others. Always a competitor, and always the man... Even if I did get this one interception in HS. This picture means a lot to me for the moment we shared among many others. I will NEVER forget James Hardy. He is missed. Prayers to his family, friends, and all our fellow teammates. #IUFB
Hardy appeared in 16 games (three starts) in his NFL career, catching 10 passes for 96 yards and two touchdowns.
He was arrested in Los Angeles for resisting arrest in 2014 but a judge later ruled him not mentally competent to stand trial.