As a professional cleaner, people often ask me cleaning related questions. I am always happy to answer any cleaning questions on the table because I know I will still have a job – there are quite honestly many people who will continue to be too busy to clean or who will simply not want to.
One of the main problems people want information about is how to remove hard water stains from a toilet. I run into landlords frequently who have had a tenant that never cleaned the toilet and consequently there is now a permanent-looking rust ring inside the bowl. I tell them not to despair, their rust problem is easily solved with the right chemicals and a little patience.
If you have this problem, you need to know that hard water stains are alkaline mineral deposits. In order to remove alkaline stains, you need a chemical solution that is moderately to severely acidic. Often people give up on the problem after using 
greenphactor household toilet bowl cleaning products purchased from the grocery store. The thing is: they simply aren’t strong enough to break down the minerals.
What you need is something stronger. There are a variety of products that could work for you. You could try Bar Keepers Friend which is powdered oxalic acid. This is readily available from many stores, by the way. Or you could use CLR (calcium, lime, and rust remover) or Lime Away which contain phosphoric acid. In really extreme cases, you will want to use straight muriatic acid. For any of these solutions, however, make sure to wear rubber gloves and goggles, and to open the bathroom door (and window if possible) and to turn on the overhead fan.
Now, when you have the solution that you want to use, one way to make sure it is full strength is to empty the toilet bowl. To do this, you can either shut of the water supply to it by turning a knob at the base of the toilet and then flushing it, or you can pour a bucket of water into the bowl.
Once you have the bowl empty, don your protective gear, and apply the acidic solution to the toilet bowl. I would recommend carefully pouring it onto a green abrasive sponge and then scrubbing it around the bowl. If the ring immediately comes off, congratulations, you are done. If it doesn’t, let the solution dwell for 30 min to an hour. I have never seen this fail to make a toilet sparkling white again. One more thing, if you are worried about flushing the acidic solution into your septic or the cities sewer system, you will want to neutralize the acid after you are done by mixing a hefty amount of baking soda into the bowl (a half box to a box) and letting it sit for a couple of minutes before finally flushing.