The Grammy-winning singer made the announcement at a show in the state on Saturday night.
Mars said he and tour promoter Live Nation would redirect funds from the performance at Auburn Hills to the Community Foundation of Greater Flint.
The charity in part supports residents affected by lead-contaminated drinking water, which led to a state of emergency being declared in 2014.
Experts also linked 12 deaths from a Legionnaires' disease outbreak to the improperly treated water.
In a statement, Mars said: "I'm very thankful to the Michigan audience for joining me in supporting this cause.
"Ongoing challenges remain years later for Flint residents, and it's important that we don't forget our brothers and sisters affected by this disaster."
Mars, who was born and raised in Hawaii, is currently travelling across the US for his 24K Magic World Tour. His latest album 24K Magic recently achieved double platinum status.
The Flint water crisis began in 2014 when the source of the city's water supply was switched to the Flint River. Due to insufficient water treatment, it was later found to contain dangerous levels of lead.
A state of emergency was declared in January 2016 and residents were urged to drink bottled water instead. Replacement of lead pipes is not expected to be completed until 2020.
US President Donald Trump commented on a visit to the midwestern state: "It used to be that cars were made in Flint and you couldn't drink the water in Mexico.
"Now cars are made in Mexico, and you can't drink the water in Flint. That's terrible."