Residents of the city were left with lead-contaminated water, which was blamed for a deadly outbreak of Legionnaires’ disease that killed 12 people.
Snyder, a Republican, becomes the first governor or former governor charged with crimes relating to their administration in the state’s 184-year history.
The misdemeanor charges, filed by the state’s attorney general Dana Nessel, carry a punishment of up to a year in prison and a $1,000 fine.
It is expected that charges will also be filed against former officials who served as state health director and as a senior advisor, reports the Associated Press.
The majority Black city’s water issues began in 2014 when a Snyder-appointed manager made a money-saving decision to use water from the Flint River, while a pipeline from Lake Huron was under construction.
But the corrosive water was not treated properly and released lead from old plumbing in homes.
Despite pleas from residents it took Mr Snyder’s administration 18-months to take significant action after a doctored reported elevated lead levels in Flint children.
Residents were forced to line up for bottled water with parents left worried their children may have suffered permanent health damage.
Authorities have now replaced 9,7000 service lines at homes in the city and Flint’s water, which comes from a Detroit regional agency, now gets good marks.
The Associated Press contributed to this report.