[2] He graduated from Harvard University in 1855, subsequently studying engineering and chemistry, and taking the degree of Bachelor of Science at the Lawrence Scientific School of the same institution in 1857; in 1859 became an assistant in the United States Coast Survey.

[2] E. J. Hulbert, a friend of Agassiz's brother-in-law, Quincy Adams Shaw, had discovered a rich copper lode known as the Calumet conglomerate on the Keweenaw Peninsula in Michigan.

With insufficient supplies at the mines, Agassiz struggled to maintain order, while back in Boston, Shaw was saddled with debt and the collapse of their interests.

[6] Shortly after the death of his father in 1873, Agassiz acquired a small peninsula in Newport, Rhode Island, which features views of Narragansett Bay.

He was a member of the scientific-expedition to South America in 1875, where he inspected the copper mines of Peru and Chile, and made extended surveys of Lake Titicaca, besides collecting invaluable Peruvian antiquities,[2] which he gave to the Museum of Comparative Zoology (MCZ), of which he was first curator from 1874 to 1885 and then director until his death in 1910, his personal secretary Elizabeth Hodges Clark running the day-to-day management of the MCZ when his work took him abroad.

[7][8][9] He assisted Charles Wyville Thomson in the examination and classification of the collections of the 1872 Challenger Expedition, and wrote the Review of the Echini (2 vols., 1872–1874) in the reports.

However, in 1865, he published with Elizabeth Cary Agassiz, his stepmother, Seaside Studies in Natural History, a work at once exact and stimulating.

Alexander Agassiz is commemorated in the scientific name of a species of lizard, Anolis agassizi, and a fish, Leptochilichthys agassizii.