His sister Frances (Fanny) married Dr Henry Pilkington Drummond, of Silent Street, Ipswich: his brother Dr. Edward Clarke, also a medical student, produced architectural drawings for the papers of the short-lived Suffolk Archaeological Association.
The family life is described by Henry Button (born 1829, son of Clarke's half-sister Harriet, née Lloyd), who lived in the household as a child after his parents and brethren emigrated to Launceston, Tasmania in 1833, until joining them in 1837.
Henry was taught to read by his aunts, and joined his uncle William (who carried a percussion fowling-piece or a "gunstick") on country excursions up and down the rivers Orwell and Gipping in search of natural history specimens for taxidermy.
[20] In 1837 Dr. Clarke contributed an article to the Magazine of Natural History describing his discovery of an Argentine (a fish then seldom recorded in British waters) at Portobello on the Firth of Forth in April 1833.
As it progressed, through the concerted energies of the Quaker Alexander and Ransome families, and under the direct scientific guidance of Professor Henslow (Charles Darwin's friend and mentor), Clarke was rather belatedly invited to be its first Curator.
With his assistant William Bilson he was also responsible for taxidermy of many specimens, and had the somewhat disagreeable task of stuffing the carcass of a lion named "Wallace" (obtained from Wombwell's Menagerie) during a hot summer.
[29] In 1849 he published on a species of zoophyte discovered in the New Dock at Ipswich (with illustrations by his co-author engraved on wood by Edward Clarke),[30] and also reported on a bottlenose dolphin lately found at Bawdsey, which had been sent to him at the Museum.
[31] It was during a dredging expedition on the river Orwell, on behalf of the Museum, that he met with a sailor named Nunn who, being engaged in the whale fisheries during the 1820s, had had the interesting misfortune to be marooned on the remote Southern Ocean archipelago of the Kerguelen Islands for three years.
Recognizing the scientific importance of a first-hand testimony of this comparatively unknown place, Clarke took down his story at length and raised an advance subscription from among the many patrons and sponsors of the early Museum.
[34] He was taunted by Ipswich youths who threw lighted squibs outside his office door, or urinated in the Museum doorway, infuriated by boys who banged the cases underneath to make specimens fall off their stands, or spat fruit pips from the balcony onto the polished glass table-cases beneath, and morally outraged by the conviction that the free evening public lectures in the Museum were being used by disreputable persons to make informal romantic assignations which were forthwith consummated in a neighbouring garden.
[36] He considered that Henslow had made insufficient acknowledgement of his part in identifying the deposit in which the phosphatic nodules of the Crags – the foundation of the Coprolite industry – had been recognized at Felixstowe.
Hooker's copy of the Wreck of the "Favorite", wrote to Henslow in November 1854 asking him to find out from Dr. Clarke whether John Nunn could say what sorts of driftwood were found in Kerguelen.