Water naturally contains minerals and leaves deposits, called lime scale, in toilet bowls or any other water-holding vessel. This stains areas of the toilet bowl a yellow to light rust colour that leaves the bowl looking dirty. Because this is such a common problem, there are products sold commercially that will remove these deposits--however you can use a home remedy that is less costly and less caustic than these.
Turn off the water valve to the toilet. This is usually a knob or lever near the back of the toilet.
Put on rubber gloves.
Flush the toilet several times to lower the water level, then use a cup or pail to remove the rest of the water from the bowl. The cleaner you will be using works better and faster if it isn’t diluted by the water in the bowl.
Saturate paper towels with white vinegar. Place these over all the areas stained with lime scale, as suggested by Mrs. Clean USA. Pour the rest of the first gallon of white vinegar into the toilet. Leave it for two to three hours (or overnight).
Check beneath one of the paper towels to see if the stain is easily coming off. Remove the paper towels and scrub the stain with them. If any hint of stains remains after scrubbing, wet new paper towels with the vinegar and replace in the toilet. Add the rest of the vinegar solution and leave this for several more hours or overnight.
Remove the paper towels. Scrub the toilet with a clean scrub brush. Use a new brush to avoid interactions with cleaning products (that may have left residue on old brushes).
Turn the water back on to the toilet, letting it fill. Scrub the toilet again when it has filled. Flush the toilet twice to rinse it.
If any stains persist, Stain Expert (ref. 2) suggests scrubbing the bowl with bleach or borax. Just as with the vinegar, these products should be left on the interior bowl surface for a while (30 minutes to several hours) before you scrub it and flush the bowl.
Do not mix vinegar or other solutions with bleach toilet cleaning solutions--this may create toxic fumes.