Right, there's no official rule on the matter.
I'd say roll the damage as normal (1d10 per 10 feet) and then halve it. An acrobatics check can then reduce that damage as normal, since you only need to make yourself fall vertically instead of doing that and also trying to land safely.
I think it's also worth to discuss how deep you end up plumetting into the water after the fall, and what happens if you plumett all the way to the bottom. I would say that you sink half the distance you fell and if you hit the bottom before sinking all the way, take the rest of that distance as normal falling damage (so, falling from 40 feet into 10 foot deep water would make you take 4d10/2 damage, then sink 20 feet, but since it is only 10 feet, you sink to the bottom and take 1d10 damage, since you had 10 feet left to go. Example dice say you'd take 20 damage in all. Seems about right). This is based on random ideas and no science whatsoever.