The 12 residents of the predominately African-American community died after city officials implemented a cost-cutting plan in 2014 to switch the water supply to the contaminated Flint River.

Authorities say at least 90 cases of Legionnaires’ disease are also linked to the plan.

Nine former state and local officials pleaded not guilty in Genesee County courts on Thursday to a total of 42 criminal counts.

The charges are the culmination of a years-long criminal investigation that ran parallel to civil litigation.

The civil proceedings last year yielded a settlement worth more than US$600 million ($771 million) for victims of the water crisis.

Wayne County prosecutor Kym Worthy said she and her colleagues reviewed millions of documents and drew on the expertise of external epidemiologists.

“Pure and simple this case is about justice, truth, accountability, poisoned children, lost lives, shattered families that are still not whole and simply giving a damn about all of humanity,” she told a news conference in Flint.

All charges stemmed from evidence presented to Judge David Newblatt, who served as a secret one-person grand jury.

Former state health director, Nick Lyon, and former state medical executive, Eden Wells, were each charged with involuntary manslaughter.

It’s the second time that the pair have been charged with manslaughter.

They were accused in 2017 of failing to warn the public about the outbreak in a timely manner, but the cases were dropped by prosecutors.

An involuntary manslaughter conviction carries up to 15 years in prison and a $7,500 fine.

Snyder is facing misdemeanour charges of wilful neglect of duty in Flint.

He is the first governor or former governor in Michigan’s 184-year history to face charges related to time in that office.

Special prosecutor Fadwa Hammoud, of the Attorney-General’s office, declined to offer details during a news conference, but said Mr Snyder had “failed to protect the health and safety” of Flint’s nearly 100,000 residents.

“There are no velvet ropes in our criminal justice system,” Hammoud said.

“Nobody — no matter how powerful or well-connected — is above accountability when they commit a crime.”

Hammoud said their ongoing grand jury investigation could yield additional charges.

“The Flint Water Crisis is not some relic of the past,” she said.

“At this very moment the people of Flint continue to suffer from the categorical failure of public officials at all levels of government.”

Wearing a mask, Snyder, 62, said little during his brief hearing, which was conducted by video.

Each of the two counts he faces carries a maximum penalty of a year in jail and a $1,000 fine.

The indictment against Snyder alleges that he failed to check the “performance, condition and administration” of his appointees and protect Flint from disaster when he knew the threat.

Despite desperate pleas from residents holding jugs of discoloured water, the Snyder administration took no significant action until a doctor reported elevated lead levels in children about 18 months later.

Lead can damage the brain and nervous system, and cause learning and behaviour problems.

Flint’s woes have been highlighted by activists as an example of environmental injustice and racism.

Prosecutors charged emergency manager, Darnell Earley, with misconduct in office.

Rich Baird, a friend and close adviser to Snyder, was charged with extortion, perjury and obstruction of justice. He’s also accused of lying during an interview with Flint water investigators in 2017.

Jarrod Agen, who was communications director before going to work for Vice-President Mike Pence, was charged with perjury.

Former Flint public works director, Howard Croft, was charged with wilful neglect of duty.

Nancy Peeler, of the state health department, was charged with misconduct in office for allegedly concealing a blood-lead level analysis of children.

Defence attorney Brian Lennon called the case a “travesty”.

“These unjustified allegations do nothing to resolve a painful chapter in the history of our state,” he said in a written statement.

“Today’s actions merely perpetrate an outrageous political persecution.”

Separately, the state, Flint, a hospital and an engineering firm have agreed to a US$641 million ($771 million) settlement with residents over the water crisis.

A judge says she hopes to decide by January 21 whether to grant preliminary approval.

Other lawsuits, including one against the US Environmental Protection Agency, are pending.