Hard water stains in toilet bowls are caused by calcium and magnesium dissolved in tap water from municipal water systems and private wells. These minerals form off-white, gray or pinkish scaly deposits on the inner surfaces of the toilet bowl. The deposits don't endanger health, but they look nasty. Water softeners often remove most, but not all, the dissolved minerals in your water. If you have hard water, sooner or later you will need to remove these ugly mineral stains.
Clean the toilet bowl with the stiff-bristled toilet bowl before you remove the hard water deposits. After cleaning and flushing, turn off the water supply valve to the toilet clockwise until it stops turning. The valve is typically located slightly above the floor on the water supply line to the tank at the back of the toilet. Flush the toilet and use the plunger to remove as much water as possible.
Put on rubber gloves. Squirt an acid-based liquid toilet bowl cleaner directly onto the mineral deposits staining the surfaces of the toilet bowl, making certain to get some cleaner under the rim. Allow the product to sit on the stains and work in for a few minutes. Several different cleaner brands are available in grocery and hardware stores. Commercial products typically use hydrochloric acid, also known as hydrogen chloride or muriatic acid. Some products even use phosphoric acid or sulfuric acid as their active ingredient.
Remove the mineral deposits by brushing the bowl surface with a toilet brush that has stiff nylon bristles. Pay particular attention to the water inlets under the rim and at the base of the bowl. If hard water stains remain, apply more bowl cleaner and repeat the cleaning process until the stains are completely gone. Work slowly to avoid spatters that can burn your skin and harm other bathroom surfaces. When done cleaning, turn on the water supply to the toilet and allow the flush tank to fill. Close the toilet's lid and flush the toilet to rinse the cleaner out of the bowl. These same steps work for rust or red-brown stains, a result of high iron content in the water, which often accompany hard water scaly deposits, especially in homes with private or rural wells.