[3] After graduation in 1839, he continued to study chemistry in Philadelphia, and in 1840 he joined a geologic survey of New Hampshire as an unpaid assistant to Charles T. Jackson.

When Whitney returned home in 1847, he and John Wells Foster were hired to assist Charles T. Jackson in making a federal survey of the Lake Superior land district of northern Michigan which was about to become a major copper and iron mining region.

Building on this experience, Whitney became a mining consultant, and eventually wrote the book, Metallic Wealth of the United States (1854).

Whitney tactlessly complained, telling legislators: We have escaped perils by flood and field, have evaded the friendly embrace of the grizzly, and now find ourselves in the jaws of the Legislature.In 1867, the survey was eliminated from the budget, and work was suspended in 1868.

Although the California Geological Survey ceased work when funds were eliminated, Whitney managed to retain the title of state geologist until 1874.

The state funded the publication and printing of the first three volumes of the survey's results, and Whitney published the remaining reports using his own money.

The second controversy involved the discovery of the Calaveras Skull, allegedly uncovered by a miner 130 feet (40 m) beneath the surface of the earth.

The third controversy involved the dispute over California's potential oil wealth with Yale Professor Benjamin Silliman Jr. After conducting a small-scale survey of surface seeps of petroleum in Ventura County, Silliman claimed that California possessed "fabulous wealth in the best of oil".

Whitney devoted much of his time and energy to personally attacking and discrediting Silliman, whose reputation was severely tarnished over the course of the public debate between the two.

Whitney married Louisa Goddard (born in Manchester, England, December 17, 1819; died in Cambridge, Massachusetts, May 13, 1882) on July 5, 1854.

She wrote The Burning of the Convent: a Narrative of the Destruction of the Ursuline School on Mount Benedict, Charlestown, by One of the Pupils (Cambridge, Massachusetts, 1877), and Peasy's Childhood: an Autobiography (1878).