IIRC the problem with flint michigan water was high lead concentration, which isn't something that's as visible as the gp described. I can see how elevated lead levels can fly below the radar, but not brown water.
Might just be an issue with nearby pipes, and not something affecting the entire supply. When the municpal water pipes get cleaned around where I live, they put up signs saying that your water might be brown or rust colored for a few days, but to just let the tap run for a few seconds before you start drinking it or showering.