How to Stop the Mineral Discoloration in a Toilet With Well Water

Well water often has an elevated mineral content, with iron high on that list. High levels of iron in water can leave stains on even the smoothest, most stain resistant surfaces, such as toilets. Toilets are constructed from glazed ceramic clay, which is highly resistant to germ growth and staining, but the material still can't hold up to constant exposure to high amounts of minerals from well water, which may also contain high levels of calcium and magnesium. The resulting brownish-red stains aren't permanent, however, and can be removed quickly and prevented in the future.

Things You'll Need

  • Gallon of white vinegar

  • Acid-based toilet bowl cleaner

  • Toilet scrub brush

  • Water softener

  • Acid-based toilet cleaner puck

Step 1

Shut off your toilet's water valve, which is located behind the toilet. After you've shut off the valve, flush the toilet to remove all the water. You'll want to remove existing stains to stop further stains from forming, and your cleaning efforts will be much more effective without a gallon of water diluting your cleaning solutions.

Step 2

Pour about a gallon of vinegar into the toilet, or however much you need to fully submerge all your mineral stains. Allow the vinegar to sit for several hours, preferably overnight. The vinegar will help remove any lime deposits, which are caused by calcium and magnesium, by softening them. Scrub at the stains with your brush to remove as much as possible.

Step 3

Turn on the water valve so you can flush the vinegar down the toilet. Turn off the water valve again to proceed.

Step 4

Apply your acid based toilet bowl cleaner directly to the stain. You'll have far more luck removing your well water stains using an acid-based cleaner instead of a chlorine-based cleaner, because chlorine-based cleaners don't remove iron stains.

Step 5

Allow the cleaner to sit for a few minutes, and then start scrubbing with your scrub brush. The stains and deposits should start coming off right away. Continue cleaning until you've removed all the stains. Apply more cleanser, if necessary.

Step 6

Turn on the water to flush the toilet and complete the cleaning portion of your efforts to stop your toilet's mineral discoloration.

Step 7

Install a water softener, which will reduce the amount of iron, calcium and magnesium in your water. You'll want to install your water softener into your home's water supply system. The device needs to be kept safe from the elements and moisture. Choose a level area, preferably a concrete surface. Install a well water softener in your well water system's pressure tank. Softer water will keep your toilet from staining.

Step 8

Attach your toilet puck to the inside of your toilet bowl. The puck will help stop future discoloration.


Clean your toilet frequently. The more often you clean your toilet, the less often hard to remove stains will form. Even with well water, a regular cleansing with a swipe of acid-based cleanser will stop toilet bowl mineral discoloration.


Wear neoprene elbow length gloves and protective eye wear when cleaning with any acid-based cleanser.

References & Resources