From 1976 until March 1979, she served as the U.S. Navy's Pay and Allowance Functional Manager at the Bureau of Naval Personnel (PERS-3) in Washington, D.C. She was selected to be one of the first women officers in Surface Warfare and in 1979 graduated number one in her class at the Surface Warfare Officer Basic Course in Newport, Rhode Island.

Further assignments included a tour on the destroyer tender USS Yellowstone (AD-41), where as a lieutenant commander Loewer served as engineer and executive officer, and on board the fleet oiler USS Monongahela (AO-178), where she served as executive officer.

In September 2000, she was requested for a return tour of duty as the military assistant to Secretary Cohen.

She became vice commander of the Military Sealift Command in July 2003, headquartered in Washington, D.C. as such, Rear Admiral Loewer was second-in-command of a global transportation agency with a workforce of more than 8,000 and a fleet of more than 120 active ships whose primary mission is to move U.S. military cargo for deployed U.S. forces.

On September 11, 2001, between 8:46 a.m. and 8:55 a.m., Loewer was traveling in President Bush's motorcade toward Booker Elementary School when she learned of the first crash of an airplane into the World Trade Center from her deputy in the Situation Room at the White House.