Heading east from San Diego, the survey parties traveled through some of the most rugged and remote terrain in the country.

Whipple was directed to lead one of those surveys along the 35th parallel from Fort Smith, Arkansas to Los Angeles.

The Whipple expedition left Fort Smith on July 15, 1853, with a group of seventy men including soldiers, teamsters, and scientists.

Among the scientists were John Milton Bigelow, a medical doctor and botanist; Jules Marcou, a Swiss geologist; and Balduin Möllhausen, a German artist and a protege of Alexander von Humboldt.

[1][4] After Albuquerque, they were joined by frontiersman Antoine Leroux who helped to guide the surveyors through the most difficult part of the journey to California.

In addition to reports on topography, geology, botany and zoology, Whipple wrote a lengthy essay on the southwestern Indian tribes that the expedition had encountered.

[5] Whipple was promoted to captain in 1855 and then assigned to supervise efforts to open the Great Lakes to navigation by larger vessels, deepening channels through the St. Clair flats and the St. Mary's River.

[6] At the outbreak of the Civil War, Whipple served for a time under General Irvin McDowell as commander of the nascent balloon reconnaissance unit.

He was later awarded posthumously more brevets for his wartime services, and both of his sons received presidential appointments to the military academy of their choice.