Eugene lawyer Dan Koenig said Tuesday that he sent the notice of Masoli's not-guilty pleas last week.
Masoli was cited June 7 for possessing less than an ounce of marijuana, driving with a suspended license and failing to stop when entering a roadway. No trial date has been set.
Masoli pleaded guilty in a January theft at a fraternity house and was suspended for the entire upcoming season by Oregon coach Chip Kelly.
Masoli was kicked off the team on June 9. The university said he was dropped because he didn't "adhere to obligations" outlined by Kelly.