Best way I have found to remove the brown water line stains is a product called On/Off. Put some in a garden sprayer, spray it on, let sit for a minute or 2 (don't let dry) rinse off and you are done.
Also works great for disolving the white patches left after scraping barnicles.
This stuff is really toxic so you need to be careful to use gloves, wear eye protection and be careful not to breath it in.
Muratic Acid found in Home Depot (NS

) is supposed to work the same but I'm told is not as strong.