Powell was appointed by US President James A. Garfield to serve as the second director of the U.S. Geological Survey (1881–1894) and proposed, for development of the arid West, policies that were prescient for his accurate evaluation of conditions.

[3]: 89  At the Battle of Shiloh, he lost most of his right arm when struck by a Minié ball while in the process of giving the order to fire.

Despite the loss of an arm, he returned to the Army and was present at the battles of Champion Hill, Big Black River Bridge, and in the siege of Vicksburg.

Powell helped expand the collections of the Museum of the Illinois State Natural History Society, where he served as curator.

[16] In planning this expedition, he employed the services of Jacob Hamblin, a Mormon missionary in southern Utah who had cultivated relationships with Native Americans.

In 1881, Powell was appointed the second director of the U.S. Geological Survey, a post he held until his resignation in 1894,[3]: 394, 534  being replaced by Charles Walcott.

[16]: 48, 50–51, 53, 55, 57, 59, 63, 93, 107 Powell spent time among the Native Peoples of the Colorado Plateau and wrote an influential classification of North American Indian languages.

[19]: 340  From 1894 to 1899, Powell held a post as lecturer on the History of Culture in the Political Science department at the Columbian University in Washington, D.C..[20] He was elected a member of the American Antiquarian Society in 1898.

For example, in 1873, in response to tensions surrounding the Modoc War, he temporarily left the Survey to serve as special commissioner for the Department of the Interior.

Powell and co-commissioner George Ingalls delivered a report in December of that year recommending a program to relocate members of the Ute, Paiute, Shoshone, and Western Shoshone peoples to reservations where, Powell and Ingalls hoped, they would practice Western-style agriculture and be insulated from further conflicts with white settlers.

"[3]: 285 After Powell assumed near-permanent residency in Washington, D.C. as director of the Bureau of Ethnology and the U.S. Geological Survey, his contributions to anthropology consisted increasingly of hiring others to conduct field research and abstract theorizing.

[3]: 451–55  [22]: 107-10 As many scholars have noted, Morgan's hierarchical schema was often used to justify the dispossession of Native peoples and to support theories of racial difference.

[23] Indeed, the study of ethnology was often a way for scientists to demarcate social categories in order to justify government-sponsored programs that exploited newly appropriated land and its inhabitants.

[24][23][25] Believing that "progress" was linear and inevitable, Powell advocated for government funding to be used to 'civilize' Native American populations, pushing for the teaching of English, Christianity, and Western methods of farming and manufacture.

[26][21] However, Powell was not a Social Darwinist; his schemes for cultural assimilation and resource sharing in the Arid Region called for complex government intervention, a far cry from the libertarianism advocated by people like Herbert Spencer.

As an adult, Powell seems to have believed (in line with Morgan's theory of social development) that Native Americans embodied a more "primitive" phase of human society than that of their white European counterparts.

For example, in The Exploration of the Canyons of the Colorado, he describes the subsistence practices of a group of Indians "more nearly in their primitive condition than any others on the continent with whom I am acquainted.

"[27] Although, as Wallace Stegner observes in Beyond the 100th Meridian, by 1869 many Native American tribes had been pushed to extinction, and many of those who survived had experienced significant intercultural exchange.

[30] Powell's expeditions led to his belief that the arid West was not suitable for agricultural development, except for about 2% of the lands that were near water sources.

They aggressively lobbied Congress to reject Powell's policy proposals and to encourage farming instead, as they wanted to cash in on their lands.

Thomas suggested that agricultural development of land would change climate and cause higher amounts of precipitations, claiming that 'rain follows the plow', a theory which has since been largely discredited.

"[32] Powell's recommendations for development of the West were largely ignored until after the Dust Bowl of the 1920s and 1930s, resulting in untold suffering associated with pioneer subsistence farms that failed because of insufficient rain and irrigation water.

[42][43] On November 28, 1861, while serving as captain of Battery 'F' of the 2nd Illinois Light Artillery at Cape Girardeau, Missouri, he took a brief leave to marry Emma Dean.