Waters was ordained to the priesthood for the Diocese of Richmond in Rome by Cardinal Francesco Selvaggiani on December 8, 1931.

In 1953, a year before Brown v. Board of Education decision by the US Supreme Court, Waters ordered the desegregation of all Catholic churches and schools in the diocese.

"[6] Bishop Michael Begley said of Waters, "[his] missionary zeal and his concern for God's people cannot be measured.

Waters was later accused by some of the diocesan clergy of holding on to idle church property worth millions of dollars while some parishes were in debt.

[3] In 1972, Waters expelled five Sisters of Providence nuns from the diocese for not wearing their religious habits while teaching.