Davis spent two years at Harvard before becoming a midshipman, and he returned there for the study of mathematics between sea cruises. He made the first comprehensive survey of the coasts of Massachusetts, Rhode Island, and Maine, including the intricate Nantucket shoals area. He also was a prime mover in establishing the American Nautical Almanac (1849), supervising its preparation for several years. A tireless worker for scientific progress, Davis was one of the founders of the National Academy of Sciences in 1863. He also wrote several scientific books.

During the American Civil War, he was a member of the board that recommended building the Monitor and was with Admiral Samuel F. du Pont at Port Royal. Then he commanded the Union gunboat flotilla on the upper Mississippi for several months after Commodore Andrew Hull Foote was injured in February 1862. A practical officer, he became a rear admiral in 1863.