Black stains inside toilet tank

Sounds like manganese, in the water…

“Water coming from wells and springs with high iron and/or manganese may appear colorless initially but orange-brown (iron) or black (manganese) stains or particles quickly appear as the water is exposed to oxygen (see Water Testing).”

From: http://extension.psu.edu/natural-resources/water/drinking-water/water-testing/pollutants/iron-and-manganese-in-private-water-systems