Holidays and Traditions How do you clean a heavily stained toilet bowl? How do you clean a heavily stained toilet bowl? - Pour 1 or 2 cups of white distilled vinegar into the toilet bowl. - Sprinkle some baking soda. You will get a sizzling reaction. - Wait about 15 minutes. - Scrub the stains with your brush or pumice stone. - Turn the water back on and flush. Related Posts:How to remove yellow stains from toilet seat and bowl.How to remove yellow stains from toilet bowl and seatHow do I get rid of water build up in my toilet?There are 4 ways to remove paint from the house.