That's the deal.
Usually gotta aim completely below the fish.
Sometimes several fish-widths lower.
It feels very wrong for an archer to aim THAT low, but that is how it works.

JC has the right idea for practice.
Shoot at things that are submerged preferably on the bottom, and then evaluate where your shot hitbefore you reel it in. Were you on-line left to right? Were you high or low?

How much you need to compensate depends on how deep the fish is, and how far out it is from you. The steeper the viewing angle, the more direct of a shot you can take. That's why everybody builds platforms on their boats -to get up higher and see better into the water, and have less severerefraction to deal with. Even 6 inches of elevation can make a pretty noticeable difference.

Once you get it, it'll become second nature.