The 18-time Olympic gold medalist was stopped in the early hours of the morning after being clocked by police doing 84mph in a 45mph zone.
A statement from Maryland Police revealed that an officer saw Phelps' vehicle speeding within the Fort McHenry tunnel in Baltimore and proceeded to follow it before pulling him over.
Phelps, who was described as "cooperative throughout the process", was identified by his driving license and "was unable to perform satisfactorily a series of standard field sobriety tests".
He was consequently arrested and charged with driving under the influence, excessive speed and crossing double lane lines, before later being released.
It is not the first time the swimmer has been in trouble for drunken driving, in 2004 he pleaded guilty to driving while impaired and was fined $250 and ordered to serve 18 months' probation.
Phelps returned to swimming in April having retired following his four gold medals at London 2012 and claimed three wins at the Pan Pacific Championships last month.
He issued an apology for his actions later on Tuesday via his official Twitter account.
"Earlier this morning, I was arrested and charged with DUI, excessive speeding and crossing double lane lines," wrote Phelps.
"I understand the severity of my actions and take full responsibility.
"I know these words may not mean much right now but I am deeply sorry to everyone I have let down."