Dark stains can appear inside the bottom of a toilet bowl due to hard water or particles from your home's water supply. Toilet cleaning products that are placed inside the bowl's water may remove stains on the side of the bowl, but these products will likely not be effective on stains on the bottom of the bowl. Removing the water in the bowl and using a homemade bowl cleaner takes such stains away and removes bad odors.
Turn the shutoff valve found under the toilet clockwise until it will no longer turn. The toilet's water now is shut off.
Flush the toilet. Plunge the toilet's drain until there no longer is any water found in the toilet.
Pour ¼ cup baking soda into the bottom of the toilet. Add 1 cup of undiluted white distilled vinegar into the bottom of the toilet. Wait until the bubbling reaction that occurs when the vinegar touches the baking soda subsides.
Scrub the bottom of the toilet with a soft toilet brush. Leave the vinegar and baking soda at the bottom of the toilet for several hours or overnight.
Scrub the bottom of the toilet one final time. Turn the shutoff valve back on, and flush the toilet.