Last year we bought our first pool. Instead of filling it with tap water, we paid the local fire dept to bring water from the river (which is common in our area) When they dumped the first load, it was almost red with rust from their tanks. They assured me that chlorine would take care of it...WRONG!! After countless trips to the pool doctors with viles of water, gallons and gallons of bleach, chlorine tablets, and anything else I could think of, I finally left it alone.
The pool was rusty through the entire summer until the end, when I discovered a cure for the problem. After letting the pool sit for a week without any disturbance the rust settled to the bottom, leaving the water crystal clear. I then hooked up my vacuum hose to my pump and the outtake water (instead of running it back into the pool) I unhooked it and as I vacuumed, I let the rusty water flow into my back yard. This didn't take long to do the entire floor of the pool. We were left with the water level a little low, but the waterhose quickly filled it back again. There was only 1 week left to swim!!
I just wanted to share this story in case someone out there has the same problem and can't find a cure. Hope this helps.