Inspector-General of Hospitals and Fleets Sir John Denis Macdonald KCB FRS (26 October 1826 – 7 February 1908) was a naval surgeon.

As a result of his studies, principally with the microscope, on the seabed deposits brought up by the dredger he was awarded in 1862 the Makdougall-Brisbane prize by the Royal Society of Edinburgh and elected a member of the Royal Society in 1859 (his membership was proposed by Joseph Toynbee, Edwin Lankester, Francis Sibson, Richard Owen and Richard Partridge among others).

In March 1872 he was appointed to the flagship at Portsmouth for service as professor of naval hygiene at the Army Medical School at Netley, a post he continued to hold after his promotion to Deputy Inspector-General of Hospitals and Fleets in February 1875.

Following the succession of King Edward VII, he was among several retired navy officers appointed Knight Commander of the Order of the Bath in the 1902 Coronation Honours list published on 26 June 1902,[4][5] the investiture was on board the royal yacht Victoria and Albert outside Cowes on 15 August 1902,[6] the day before the fleet review held there to mark the coronation.

Macdonald was married twice; firstly in 1863 to Sarah Phoebe (d. 1875), daughter of Ely Walker of Stainland, Yorkshire, by whom he had three sons; James Alexander Walker (who died in infancy); John Denis; William Richard, and two daughter; Elyna Mary and Catherine Janet.