Could be iron/copper from the well -if- you've been adding chlorine already (depending on how much!)... Iron in water (from a well) won't even be noticeable at all and in Solution, until chlorine oxidizes the iron and changes it from Solution to Suspension. When that happens (and it happens slowly as you add low levels of chlorine, and happens way faster at high levels of chlorine), then the brown from the iron can turn you pool from clear blue to clear aqua or clear green or clear brown , depending on the level of iron etc.
Adding filters on the fill water (like a Metal Trap inline), can HELP but doubtful it removed -everything-, and even a TINY bit of iron (.01ppm) will discolor water. .3ppm is needed to stain IIRC.
Of course, I'm not saying it's iron without -validating- it and testing, but, with a well, its much more likely.. (or copper, or maganese, etc.)