Nothing is more gross and embarrassing than a dirty toilet. But what do you do when you’ve cleaned your toilet but the water is still brown? Read on to lean the reasons why the water in your toilet is brown and how to fix it. Believe it or not, mineral and rust stains in your toilet or tub — greenish stripes, a brown ring, lime scale — aren’t caused by anything you’re doing wrong in your cleaning regimen. It’s simply something in the water.