Born in New Plymouth on 10 April 1931, Waters was the son of Kathleen Emily Waters (née Morris) and Edwin Benjamin Waters. He was educated at New Plymouth Boys High School, and went on to study chemistry at Auckland University College, graduating Bachelor of Science in 1953, Master of Science with second-class honours the following year, and PhD in 1958. His doctoral thesis, supervised by David Hall, was titled The colour isomerism and structure of some copper co‑ordination compounds'.
In 1959, Waters married crystallographer Joyce Mary Partridge.