That's a tough one, there really should have been a liner installed behind the rock wall, without that I'm sorry to say you are always going to have a certain amount of leakage between the rocks no matter what product you use. Personally, I would just use standard cement mortar (with some concrete coloring to match the rocks) and liberally pack (point) it between all the joints the best I could. It may detract from the natural stack look of the rock somewhat but I don't know what else you can do at this point short of dismantling the wall, installing a liner and rebuilding it.
Fixing this issue is really going to be a hands-on type of thing, look at how the water flows and trying to fill and plug the suspect areas the best you can, then repeat, and in the end, you will likely still need to top up the water level frequently. If it makes you feel any better, big waterfalls like that are notorious for losing water through splashing and evaporation anyway even if they are perfectly sealed and thus require frequent top offs.
About the only other tip, I could offer is to make sure your rocks are very clean before mortaring in the joints, you might even want to pressure wash the areas you plan to fill if there is any moss or other loose debris (waterfall foam?) between the rocks.
The second half of this video gives a good example of how to mortar in the rock joints to get the best seal.