Mineral deposits occur when the dissolved minerals in water attach themselves to a hard surface. The longer they are allowed to sit unmolested, the harder and thicker the mineral deposits will be. Mineral deposits are alkaline, and will dissolve in acid. Commercial toilet bowl cleaners are acids that are so strong that they can burn skin and eyes, and if spilled can start a fire. I am much too cowardly to use such strong chemicals!
This is how I rid my toilet of unsightly mineral deposits:
Use a plunger to push as much water as possible out of the toilet bowl, then pour a gallon of white distilled vinegar into the toilet bowl. If the vinegar does not cover all the mineral deposits, pour in another gallon of white vinegar. If at all possible, let the vinegar work for at least eight hours, (perhaps overnight or while you are at work).
After eight hours of exposure to vinegar, the mineral deposits should be easy to scrub away with a toilet brush. If your mineral deposits are still resistant after eight hours of soaking, flush the toilet and repeat the process (and in the future, you might want to make your life easier by cleaning your toilet more frequently).