Phelps, competing in the 200 medley for the first time since taking gold at the 2012 London Olympics, showed early flashes of that elite form before running out of steam.
The 22-time Olympic medalist led through the first three lengths but tailed off and finished with a time of 1 minute, 59.76 seconds, behind Conor Dwyer (1:59.49) and Chase Kalisz (Fallston), who finished second in 1:59.53.
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Phelps, known for his strong finishing kick, lacked one in his third meet since he jolted the swimming world by coming out of retirement. He also tired noticeably in the final length in the 200 freestyle on Saturday.
His showing at the Santa Clara event, however, can be considered progress, as he increased his workload and swam more events than at his previous two meetings.
Phelps added Sunday's third-place finish to a tie for first in the 100 butterfly and second in both the 100 and 200 freestyle.
He is expected to compete at the U.S. nationals and Pan Pacific Swimming Championships in August as he eyes a possible appearance in the 2016 Olympics in Rio de Janeiro.