Following graduation from flight school, he flew CH-46 Sea Knight helicopters with HMM-165 from 1983 to 1985 at Marine Corps Air Station Kaneohe Bay, Hawaii.

Noriega made two 6-month shipboard deployments in the West Pacific/Indian Ocean, including operations in support of the Multinational Peacekeeping Force in Beirut, Lebanon.

In 1988, Noriega was selected to attend the Naval Postgraduate School in Monterey, California, where he earned two master of science degrees.

In January 2005, Noriega retired from the NASA Astronaut Corps, but continues to serve as the Manager, Advanced Projects Office, Constellation Program, Johnson Space Center.

During STS-84, Noriega logged approximately a total of 239 hours and 20 minutes in space traveling 3.6 million miles in 144 orbits of the Earth.