The best practice is shooting at submerged objects, but you run teh risk of losing an arrow to something solid, like a log.

I also practice occassionally in my basement with a fish arrow that had the barb broken off.
I shoot it at about 6 to 8 yards in to a foam target.
I have a cardboard cutout of a fish taped to the front of it, complete with an eye and gill line.
It doesn't help account for the water's refraction, but it at least keeps me in practice for getting my arrows to hit where I'm aiming. Since fishing arrows are so heavy, there is a lot of drop to account for, even at short bowfishing ranges.

I always try to hit fish right behind the gill because many times their head is too tough, and if you hit them too far back they can rip the barb out when they flail their tail around.