In 1990, Waters was awarded the New Zealand 1990 Commemoration Medal. In the 1995 Queen's Birthday Honours, he was appointed a Knight Bachelor, for services to tertiary education.
Waters was conferred with honorary Doctor of Science degrees by the University of East Asia in 1986, and Massey University in 1996. He was elected a Fellow of the New Zealand Institute of Chemistry in 1977, Fellow of the Australian and New Zealand Association for the Advancement of Science in 1979, and Fellow of the Royal Society of New Zealand in 1992.