Waddell was born in Pittsboro, North Carolina. He joined the United States Navy as a Midshipman in September 1841, and later graduated from the United States Naval Academy. His nearly two decades in the U.S. Navy included early service in USS Pennsylvania, Mexican-American War operations off Veracruz aboard USS Somers, a tour off South America in USS Germantown, an assignment as a United States Naval Academy instructor, eastern Pacific duty in USS Saginaw and a cruise with the East Indies Squadron with USS John Adams. Lieutenant Waddell resigned his commission while returning home in the latter ship late in 1861 at the outbreak of the American Civil War and was dismissed from the U.S. Navy in January 1862.