Baking soda is a natural deodoriser, and works by absorbing smells and excess moisture. Just sprinkle a little in your shoe to lightly cover it, and leave it overnight so it can get to work.
So, one way to limit the stains is through use. Occasionally, use or flush each toilet in your house. This will only help with decreasing the hard water stains. Issues with poor “aiming” may still ...