He was awarded a rappel to the grand prix for architecture at the Paris Exposition of 1867. In 1878 he received the Royal Gold Medal of the Royal Institute of British Architects. Waterhouse first exhibited one of his designs at the Royal Academy of Arts in 1857, and then from 1868 to 1901 with the exception of 1873 he exhibited mainly designs of his own buildings annually. But in later years he sometimes exhibited topographical views from both his British and European travels. Waterhouse was made an associate of the Royal Academy on 16 January 1878, of which body he became a full member on 4 June 1885. His diploma piece is an 1887 pen and ink drawing with colour washes, a perspective of the main facade of Manchester Town Hall and he was the Royal Academy's treasurer from 17 November 1897 to 5 December 1901. He was also a member of the academies of Vienna (1869), Brussels (1886), Antwerp (1887), Milan (1888) and Berlin(1889), and a corresponding member of the Institut de France (1893). In 1895 Victoria University of Manchester, made Waterhouse an LL.D.