If you mean the fresh water coming into the bowl when you flush is black I did have that problem. I had slightly discolored water in the galley faucet but the water in the toilet was sometimes BLACK!
To make a long story short, the cause was a deteriorated filter in the drinking water line under the galley sink that somehow was backfeeding into the regular water line. Changing the filter solved the problem.
'14 Winnebago Vista 35F, '14 GMC Terrain
BlueOx Towing Pkg, SMI Stay-n-Play
49 States & 7 Provinces visited in MH | WIT W112365