In the spring of 1849 he was assigned as second in command of the Howard Stansbury Expedition to explore and survey the Valley of the Great Salt Lake. During the trip across the plains in the spring and summer of that year, Gunnison was so ill that he was forced to ride in a closed carriage until, at Fort Bridger, he had recovered sufficiently to take charge of the party the rest of the way to the Mormon capital while Stansbury reconnoitered a new road to Salt Lake City. Lieutenant Gunnison spent the fall of 1849 in a survey of Utah Lake and the Jordan River, with the help of Mormon scientist Albert Carrington. During the winter spent in the city of the Saints, Gunnison made a study of the religion and culture of his hosts which later found publication as a book, The Mormons, a remarkably fair and balanced view for the time.
After the spring and summer of 1850 spent in the survey and mapping of the Great Salt Lake, the Stansbury party retraced its route back across the continent to St. Louis and, by the first part of January 1851, Captain Stansbury, Lieutenant Gunnison, and Albert Carrington were in Washington, D.C., where they spent the next five months preparing the maps and records for the publication of the Stansbury Report. Following this assignment, Gunnison was returned to the Great Lakes survey team where he spent the next two years, 1852 and 1853, in mapping the Green Bay area. He was promoted to captain on 3 March 1853.