brown spots in fibreglass pool

[poolgirloz]

I have a fibreglass pool. I am using water from a well/bore. It is fitted with one of those bolt on magnets that is supposed to take metals out. The spots are scattered but are worse in the corners. I have tried to scrub them but it doesn't seem to help. I am using stabilized pool chlorine with a clarifier etc in it. I have had the water tested at the local pool shop and it is often low in calcium and has low pH.
Any suggestions. I googled brown spots and I am thinking it may be Iron build up. But how do I get rid of it!