John W. Gunnison was born in Goshen, New Hampshire in 1812; he graduated from West Point in 1837, second in his class of fifty cadets. After he had served one year in the Florida campaign against the Seminole Indians, his health led him to ask for a reassignment to the Corps of Topographical Engineers, where he spent the rest of his military career. But his new appointment did not take him out of the Florida swamps for another year; in 1839 he helped to build a road in Florida until his superiors were forced to send him to Saratoga Springs in order that he could recover his health. He then finished his southern tour of duty in supervising the construction of a canal in Georgia. While there, he married Martha A. Delony on 15 April 1841.
For the next eight years, 1841 to 1849, he was engaged in survey work in the Great Lakes region. He helped plot the boundary between Wisconsin and Michigan, the western coast of Lake Michigan, the coasts of Lake Erie, and the marshy areas of northern Ohio. He was promoted to the rank of first lieutenant on 9 May 1846 but did not serve in the Mexican War, continuing with his duties as an engineer in the Great Lakes area.