Waters was appointed as a lecturer in chemistry at Auckland in 1961, rising to the rank of full professor in 1970. In 1969, he was awarded the degree of Doctor of Science by the University of Auckland on the basis of published papers submitted.
Waters served as assistant vice chancellor of the University of Auckland between 1979 and 1981, including a period in 1980 as acting vice chancellor. He left Auckland at the end of 1982, and was accorded the title of professor emeritus by the university in 1984.
In 1983, Waters was appointed as principal and vice chancellor of Massey University, serving in that role until 1995. In 1995, Massey also bestowed the title of professor emeritus on Waters.
During his career, Waters served on a range of university, science sector, and government bodies, including: the council of the Australian and New Zealand Association for the Advancement of Science from 1977 to 1979; the board of the New Zealand University Grants Committee in 1982; the New Zealand Vice Chancellors' Committee from 1983 to 1995, including periods as chair in 1984–85 and 1994; the council of Palmerston North College of Education from 1983 to 1988, the council of Manawatu Polytechnic from 1983 to 1990, as chair of the Foundation for Research, Science and Technology between 1995 and 1998; and chair of the New Zealand Qualifications Authority from 1995 to 1999.