Whenever we have any type of algae, the first thing we do here at TFP is SLAM via the
Pool School - SLAM - Shock Level And Maintain. But you must ensure you follow ALL the steps on that page and complete ALL 3 passing criteria. After that, if you still have a stain or two, let us know and we can get more specific on treatment options. The fact that you are on well water may be a reason for some of those stains as well. You may want to look at this page here:
Pool School - Metals in the Water and Metal Stains. I have a larger bit of info I will cut & paste after this post about metals for you.
Also, you might find this page helpful soon:
Pool School - Closing (Winterizing) Your Above Ground Pool.
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Some more info on metals (iron) in the water:
If your fill water is from a well, more than likely you have (metals) iron in the water. Iron comes in two forms, particles and dissolved metals. Dissolved metals don't really filter out, they either stay in suspension which is good, or precipitate out and stain your pool and water (especially when FC is increased) which is bad. The only way to remove metals is to drain and refill with metal-free water. Some folks are able to find metal free water and have it delivered, but it is costly. If the water starts to look like coffee, then it requires immediate action.
Ideally, the more “pre-filtering” of iron you can do to physically remove before treating chemically the better. Some folks have had decent success placing layers of dishrags, paper towels, or pillow batting in the skimmer to catch iron/rust particles. Others place socks or other products over the garden hose as they fill. Other methods have been used such as increasing the FC and/or PH levels to help separate the metal ions and then vacuuming and/or filtering-out the residual metal from the main filter media, but this can be risky if the metal is allowed to rest on the pool surfaces and may cause staining if not watched closely. Your best and most reliable bet is to add sequestrant to the water and replenish it periodically. Sequestrant is a chemical that binds to the iron in the water so that it can't form stains or turn brown. Unfortunately, sequestrant breaks down slowly, you need to add more regularly. ProTeam's Metal Magic and Jack's Magic the Pink Stuff (regular), the Blue Stuff (fresh plaster), and the Purple Stuff (SWG) are some of the top sequestrants. You can also find many other brands with similar products, some of which are noticeably less expensive. Sequestrants based on HEDP, phosphonic acid, or phosphonic acid derivatives are the most effective.