He conducted various zoological expeditions—in Central America for the Smithsonian Institution (1882–84), in Florida (1885), on the Saskatchewan River (1891)—and was naturalist of the Albatross Hawaiian expedition in 1902.
He was professor of zoology and curator of the Museum of Natural History of the University of Iowa from 1886 to 1890 and thereafter was head of his department.
Nutting's most important publications are systematic papers dealing with marine hydroids, which appeared in the reports of the United States Commission of Fisheries and elsewhere and were reprinted, especially American Hydroids (part i, 1900; part iii, 1915).
As museum director, Nutting was successful in attracting support from donors, politicians, university students and the public.
He organized and lead expeditions to exotic destinations, always bringing home specimens, photographs and stories to his supporters.