The charges against two state employees in the environmental department have been charged with misleading the US government about the problem.
A Flint employee is being charged with altering water test results.
Nearly 100,000 residents of the poor, mostly black city, were exposed to high levels of lead, sparking an outcry.
Lead exposure can cause learning disabilities and behavioral problems in children.
“They had a duty to protect the health of families and citizens of Flint and they failed,” said Michigan Attorney General Bill Schuette.
Bill Schuette told reporters the three individuals would face a mixture of charges including tampering with evidence, conspiracy and misconduct in office.
The two state Department of Environmental Quality employees could face up to five years in jail.
The other man charged is a local water treatment supervisor.
Bill Schuette said the charges were just the beginning of the investigation and more charges were expected with “nobody off limits”.
There have been calls for Michigan’s Republican Governor Rick Snyder to step down over the crisis.
Rick Snyder was grilled by Congress over his role in the crisis in March.
The water problems began in 2014 when the city switched its water supply away from Detroit’s water system, which draws from Lake Huron, and began to instead draw water from the Flint River.
The switch was meant to save the city millions of dollars.
However, the water from the Flint River was more corrosive than Lake Huron’s water and the pipes began leeching lead.
Seven families have filed a lawsuit against Flint authorities as some 100,000 people have been affected by the crisis.
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