Waterhouse was influenced by Pugin and most of his designs were in the Gothic Revival style. He is a prolific contributor to the design of Manchester's public, educational and commercial buildings. Waterhouse's exteriors used large quantities of "self-washing" terracotta to provide rich ornament in the polluted atmosphere and after 1880 his interiors were decorated with moulded and glazed faience both manufactured by the Burmantofts Pottery. He designed the Royal Insurance Office, in which he had an office, in 1861. The now demolished Manchester Assize Courts, built between 1864 and 1877 in the neo-Gothic style, was a major commission. In the 1860s Waterhouse designed Strangeways Gaol and its French Gothic style gatehouse in red brick with sandstone dressings and landmark tower in red brick with sandstone dressings in the style of a minaret.