Phelps, swimming for the host North Baltimore Aquatic Club, finished in 1 minute, 42.29 seconds, nearly 3 seconds ahead of Todd Patrick.
"I swam three-quarters of two real good 200s [in the freestyle and butterfly], and in the 400 IM, I was happy with that," he said.
During the meet's first two days, Phelps won the 100 backstroke, 100 butterfly, 200 freestyle and 400 individual medley.
Phelps said he will compete next with the U.S. team in this coming weekend's Duel in the Pool short-course meet in Manchester, England, against an international team of swimmers from England, Germany and Italy. After that, he plans to train for three weeks at the Olympic training center in Colorado Springs, Colo.
More than 600 swimmers from age 10 and up competed in the NBAC meet, in its 36th year. Phelps had competed here as a youth and teenager but last swam in the Annapolis event in 2004.
"We accomplished everything we came here to do," said Phelps' coach, Bob Bowman. "especially in seeing where he is in his short-course swims in relation to his best times. This meet showed he needs to be in better shape."