During his service to the university, he directed Western Carolina's moves from NAIA to NCAA Division II, then to NCAA Division I, and gained entrance into the Southern Conference. He helped raise interest in the construction of E. J. Whitmire Stadium in 1974 and Hennon Stadium in 1986. In March 1989, during the progression of amyotrophic lateral sclerosis (ALS, or Lou Gehrig's disease), Waters was reassigned from his head coaching position by university chancellor Myron Coulter. Waters died on May 29, 1989, at his home in Cullowhee, North Carolina, at the age of 50 following a six-year battle with the disease. In 1988, Waters was honored by Western Carolina, who named their playing field Bob Waters Field at E. J. Whitmire Stadium. Waters has been inducted into the South Carolina Athletic Hall of Fame, the Florida Citrus Bowl Hall of Fame, and the Western Carolina Athletic Hall of Fame.