You've got to develop a 'feel' for it.
That comes through shooting a lot, but to make the shooting productive, you have to evaluate your shot after a miss.
Was it too high or too low? Right or left?

Practice shooting at stuff on the surface first until you can get the arrows to go where you want them.
Then you can work on stuff like how far low to aim at submerged fish.
Practice on submerged objects in 1 to 4 feet of water.
Then you can try stuff like estimating how tolead moving fish.