Flint was purchasing water from Detroit. As the unemployment and poverty issues ran rampant through Detroit, less folks were paying for the water being produced. Detroit Water had to raise rates substantially to their wholesale customers, Flint being one of those. Flint decided to form a consortium with a couple other neighboring communities and put together a regional water district. The time involved in developing a new water source and building treatment facilities was years. What Detroit Water got wind that Flint was going another way, they demanded either Flint commit to remain with Detroit Water long term or they would cease delivering water to Flint in something like 90 days. Flint decided to begin pulling water from the Flint River, short term, treating it and sending it into the system.
The Flint River has been a cesspool of chemical and industrial waste for decades. Discharge from manufacturing facilities before EPA regulations... storm water runoff from closed and rundown plants along the river... No one should have attempted to treat this water to where it could be safe for drinking.
The piping in Flint... in most older communities is cast iron or ductile iron. Over time a coating develops on the inside of the old cast iron. I've seen 8" diameter cast iron water lines "grown shut" to something on the order of 2" diameter. Calcium hydroxide, iron, manganese... The minerals in the water will form a coating depending on the pH of water entering the system. Move the pH too far one way and the pipes will corrode and eventually be eaten away. Move it the other way and the minerals coat the pipes. It is a constant problem that can change a plant operation from season to season and from rain to rain.
While the heavily lead laden water was being pumped through the old cast iron lines across Flint, the lead contaminated the coating that had formed over years inside the piping. There is really no way to clean out that, now lead lining, other than replacing the piping. Over time, clean water could eventually flush/wash most of the lead downstream. But, that could take years and the water would remain contaminated during that time.
So, I really don't know how the problem will be resolved without a major water line replacement. Understand, those water lines are under streets, highways, alleys, etc. The Michigan winters will probably require a minimum of 6 FT to 8 FT bury depth. So, above these water lines and under the streets you have gas lines, fiber optic cables, telephone cables, electrical cables... all having to be protected as one excavates down to the depth required for the new line installation. I would suspect that in some of the more depressed areas of the community it would be cheaper to build homes, streets, etc. elsewhere and just abandon those neighborhoods as uninhabital. Of course, that won't happen and would simply lead to additional problems.