Snyder, a Republican who left office in 2019, was charged with two misdemeanour counts of misconduct in office.
He was the first person in state history to be charged for alleged crimes related to service as governor.
Snyder is also the eighth person to have a Flint water case thrown out after the Supreme Court's unanimous June opinion.
Genesee County Judge F Kay Behm signed the order Wednesday, a day after the US Senate approved her nomination to become a federal judge in eastern Michigan.
"The charges against (Snyder) were not properly brought and must be dismissed at this time," Behm said on Friday.
The Michigan attorney-general's office has desperately tried to keep the cases alive but so far has lost at every turn.
Prosecutors have argued the indictments could simply be turned into common criminal complaints in district court, but Behm and another judge have rejected that approach.
Flint's water became tainted with lead after city managers appointed by Snyder began using the Flint River in 2014 to save money while a new pipeline to Lake Huron was built.
The water wasn't treated to reduce its corrosive qualities, causing lead to break off from old pipes and contaminate the system for more than a year.
The water switch has also also blamed for nine deaths linked to an outbreak of Legionnaires' disease.
