Nowak received her commission from the U.S. Naval Academy in May 1985, and reported to flight school after six months of temporary duty at Johnson Space Center. She earned her wings as a Naval Flight Officer in June 1987, followed by Electronic Warfare School at Corry Station, Florida, and initial A-7 training at Naval Air Station Lemoore, California. She was assigned to Electronic Warfare Aggressor Squadron 34 at Point Mugu, California, where she flew EA-7L and ERA-3B aircraft, supporting the fleet in small and large scale exercises with jamming and missile profiles. While assigned to the squadron, she qualified as Mission Commander and EW Lead. In 1992, Nowak completed two years of graduate studies at Monterey, and began working at the Systems Engineering Test Directorate at Patuxent River, Maryland. In 1993, she was selected for both Aerospace Engineering Duty and U.S. Naval Test Pilot School. After graduation in June 1994, she stayed at Patuxent River working as an aircraft systems project officer at the Air Combat Environment Test and Evaluation Facility and at Strike Aircraft Test Squadron, flying the F/A-18 and EA-6B. Nowak was then assigned to the Naval Air Systems Command, working on acquisition of new systems for naval aircraft, when she was selected for the astronaut program.
Nowak has logged over 1,100 flight hours in more than 30 different aircraft.