Waters changed career in 1965, going to Presbyterian College as an assistant coach in 1966. After two seasons with Presbyterian, Waters moved back to the
West Coast as an assistant at
Stanford University. In 1969, Waters took a football coaching job at Western Carolina, bringing in a victorious season for the 1969 Catamounts in his first year, only losing to his
alma mater Presbyterian College. Under his guidance, the team made national rankings in 1972 and 1974, and he took the Catamounts to the
1983 NCAA Division I-AA Football Championship Game. According to the university's website, his tenure at Western Carolina produced "116 victories, 13 winning seasons and top 10 national finishes at three different levels (NAIA, NCAA Division II, NCAA Division I-AA)". He coached 13
All-Americans and 36 All-
Southern Conference players. During the 1971–1986 seasons, Waters also served as
athletic director. 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. ==Death and legacy==