You need to figure out what it is first. Rust from metal? Tanin's from tree or organic waste? Try some experiments. Cut a lemon in half. Take it down to the spot and press it against the spot for a few seconds, then try and squeeze the lemon and move it in a circle without letting water in.

Does it do anything?

Unfortunately it's all underwater right now ... - I'll look for a similar "spot" on the coping somewhere.

I believe barco meant to use the lemon underwater - just to squeeze/ press it tightly enough against the side to allow it to effectively displace the water & contact the area as fully as possible.

Yes, the lemon will work under the water. Press the cut side on the spot...squeeze it and try and keep it "water tight" under the lemon. Turn it and squeeze it some more. What happens? If its metal, then the lemon should make the stain go away or have an effect on it.

If its tanin's that comes from tanic acid and its unlikely to do much.

You have to find something that will work on your stain to come up with an "attack" plan on how to eliminate it.

Rereading your post, you said your just filling your pool...is it vinyl? If not, ask your pool builder to fix it.

IF all else fails, check out jacksmagic.com.
You can buy a stain id kit, and hen the appropriate solution to most likely remove it.
Cross your fingers its not rebar tie wire poking up through the shotcrete.