Black Water in Toilet Bowl

One reason for discolored water is due to iron and manganese bacteria. These bacteria utilize the iron and/or manganese not only in the water but in pipes and fixtures and can cause the water to turn brownish or black-brown. Sometimes it looks slimy. They do not present health-problems.

Here's a link to an Extension article from MA on the chemicals: https://ag.umass.edu/cafe/fact-sheets/iron-manganese-in-private-drinking-water-wells

Here's a link to an Extension article from PA for treatment options: https://extension.psu.edu/iron-and-manganese-in-private-water-systems