[1] Born in London, Waterhouse studied at the Royal College of Music, specifically the bassoon with Archie Camden, viola with Cecil Aronowitz, and harmony with the composer Gordon Jacob.

From 1953 to 1955, he was second bassoonist in the orchestra of the Royal Opera at Covent Garden at the time of Maria Callas, Tito Gobbi, and Kirsten Flagstad.

[4] William Waterhouse was a member of the Melos Ensemble from 1959 and participated with the group in the premiere of the War Requiem by Benjamin Britten, conducted by the composer.

He recorded all the wind chamber music by Beethoven, and works by Nielsen, Janáček, Poulenc, Schubert and Jean Françaix with the ensemble.

He wrote in 1995: "It was the remarkable rapport between this pair of lower strings" (i.e. Terence Weil and Cecil Aronowitz) "which remained constant throughout a succession of distinguished leaders, that gave a special distinction to this outstanding ensemble.

"[5] He recorded with the Melos Ensemble, its principal players Richard Adeney and William Bennett (flute), Gervase de Peyer and Keith Puddy (clarinet), Stephen Trier (bass clarinet), Peter Graeme and Sarah Barrington (oboe), Neill Sanders and James Buck (horn), Edgar Williams (bassoon), Emanuel Hurwitz and Ivor McMahon (violin), Cecil Aronowitz (viola), Terence Weil (cello), Adrian Beers (double bass), Lamar Crowson (piano):[6] In 1974 he recorded Stockhausen's Adieu with the London Sinfonietta: Sebastian Bell (flute), Janet Craxton (oboe), Antony Pay (clarinet) and John Butterworth (horn), conducted by the composer.

Players included his three children, Gervase de Peyer and Timothy Brown as former members of the Melos Ensemble, players who succeeded him such as Roger Birnstingl (Orchestre de la Suisse Romande) and Julie Price (BBC Symphony Orchestra), bassoonists from around the world, such as Jim Kopp, Lyndon Watts and Takashi Yamakami, his students and a bassoon quartet from the RNCM, led by Stefano Canuti.

[10][11] The program book includes a section of memories, titled "recollected in tranquility, a celebration", including a contribution of Karlheinz Stockhausen who wrote in 2007: Not only in rehearsal, but also in many hours before and after rehearsals and recordings, and during our trips with the ensemble, I had the pleasure and privilege of sharing with William Waterhouse his rich cultural knowledge and enthusiasm.

[18] Graham Waterhouse dedicated Mouvements d'Harmonie[19][20] and Hexenreigen[21] to him and composed Phoenix Arising for bassoon and piano[22][23] and Epitaphium as a tribute to his father's memory.