The formal regatta had its start in 1988. At that time, it was called the Bausch & Lomb Regatta, and was the first regatta to offer the unique format of head races and sprint races to competitors on the same day. Bausch & Lomb was the original sponsor of the regatta until 1995 and the regatta was run by the University of Rochester. In 1995, regatta sponsorship was passed to Stonehurst Capital and the regatta was run by the University of Rochester and RIT jointly. In 2006, Stonehurst Capital withdrew as a sponsor and the name of the regatta changed to the Head of the Genesee Regatta.

The Head of the Genesee name was first used in connection with an informal series of head races that had its start in the late 80's. At that time, a few scullers, Mike Totta and John Bernfield among them, did double head pieces on Saturday morning.  That evolved to a slightly more formalized competition (someone brought donuts) in the mid 90's. That competition typically was held the morning before the Stonehurst Regatta.

The year 2007 marks the 19th running of the regatta. 2007 also marks a change in the regatta format. A second day of racing on Saturday has been added to accomodate demand for Open, High School and Masters rowing. Collegiate racing will still occur on Sunday as in previous years.