John Waterhouse may refer to:
- Rev. John Waterhouse, general superintendent of the Wesleyan Missions in Australia and Polynesia, father of George Marsden Waterhouse
- John Waterhouse (astronomer) (1806–1879), of Halifax, inventor in 1858 of photographic equipment known as "Waterhouse stops"
- John Waterhouse (headmaster) (1852–1940), Australian educator, grandson of Rev. John Waterhouse, son of Jabez Waterhouse
- John Waterhouse (violinist) (1877–1970), Canadian violinist, conductor, and music educator
- John Waterhouse Daniel (1845–1933), Canadian physician and Conservative politician
- John William Waterhouse (1849–1917), British Pre-Raphaelite painter
- John H. Waterhouse (died 1948), American businessman and mayor of North Adams, Massachusetts