Clean out the shower pan well. Make sure any soap scum or debris is out of the pan. A mild cleanser that is not overly abrasive, such as baking soda or borax, applied with a sponge should be sufficient.
Rinse the shower pan well after cleaning.
Plug the shower pan, and then pour 1 cup of 3-percent hydrogen peroxide, lemon juice or white vinegar over the rusty area. The stain should be covered in approximately 1/2 inch of cleaning solution. Add water or more of your peroxide, lemon juice or vinegar to the shower pan if 1 cup does not adequately cover the stain.
Allow the peroxide, lemon juice or vinegar to set for about 30 minutes.
Scrub the rust stain with a nylon scrub pad or soft scrub brush and a tablespoon of baking soda or borax.
Drain the solution out of the shower pan and flush with clear water. If some of the stain still remains, repeat the treatment.