In 1977 he was elected a Fellow of the Royal Academy of Engineering, then named the Fellowship of Engineering. In 1984 he was elected president of the Smeatonian Society of Civil Engineers. In 1985 he received the Department of Defense Distinguished Civilian Service Award from the US Army Corps of Engineers in recognition of his work to secure an international agreement upon the disposal of dredged material. His wife, Margaret, died in 1991 and in 1992 he married Rachel Bishop. Harris died at East Carlton, Northamptonshire on 20 February 2005. PIANC, in conjunction with the ICE, holds an annual "Sir William Harris lecture" in his honour.
