rust from pool heater

When you get to this point it is very hard to get all of the rust out. The coating inside the steel header has worn away and then water sits in there for a period of time and causes the rust. You will always have an issue with it along with metals getting into your water of which it will be something you will have to treat the water for . At this point I would replace the unit with a new heater. The newer units have polymer headers and thus no rusting.
 
OK I understand what your saying. It's not in the budget to replace it at this time. So I'm looking for any another alternatives. I can disassemble it and clean/flush and possibly coat the rust prone parts with something if that's an option. I know it may be a bandaid fix. But I'm willing to try it for now.
 
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