OK, I think I get it now. So you use your own well water (pretreated with a little chlorine) to refill your pool's daily evaporation loss.

I'm going to guess that, while your well water is safe enough for the purposes of using it on your farm, it is not really clean enough for pool fill water. Likely what your seeing is green coming from a minor algae bloom caused by the well water and then you kill it with shock. Not the best thing to do as the shock is going to build up either excess calcium in your water or excess cyanuric acid (stabilizer) depending on the kind of shock you use (unless you're using straight bleach which is always the best).

So I think you need to pretreat the water BEFORE it goes in your pool. One way to do that would be to use a 50 gallon barrel or large container to fill with well water and then hit it with a shock level of chlorine to kill anything in it. Then after the water is treated, you can then let it into your pool. You're basically doing that now but your pool is acting as the "pretreatment" container and that's just not good. There's lots of ways to create these types of treatment barrels using large plastic drums and making hose connections into and out of it (one supply hole in the middle and three drain holes in the top). You can get fancy with ball valves and hoses and put all sorts of bells and whistles on it but the idea is the same - treat the water with high FC levels BEFORE it goes into your pool.

If you were having metal problems, then shocking your pool water when it was green would cause all kinds of staining which is not the case.