There are companies you can hire to find the exact location of the leak(s). They should also provide you with the best suggestions for repairs. What does the pool builder have to say?

That's a 1,000 gallons of water loss a day!! This is a major leak. Is any of your property wet near the pool area?

If your running the waterfalls daily, your water loss is most likely there. Try running without the waterfalls and see if your water loss changes.

Generally on any water feature, especially stone waterfalls, you can expect some water loss from splashing and evaporation.

There is no topical sealer for the stone that will stop or slow down the water loss.

Proper construction methods building a stone water fall include providing a concrete vessel/basin to set the stones and that structure must have a waterproofing material applied prior to setting any stones. This is our proven method. Any leaks that occur, stay within the vessel and don't go ant further.

We also use Acrylic 60 in our mortar mix to allow for some flexibility and movement of stones.

A heavy duty pond liner with padding is something we have used the past. It works well but prone to leaking at the edges. It's a bit tricky cut the liner at the proper locations to contain water.

We are losing an incredible amount of water. We are on average so there is room for the water to travel. It is wet all along the backside of the rocks. Not super wet but very soft. We trenched behind the weeping wall and we can see a stream of water flowing down the Gunite.

We haven’t ran the grattos in over a month to ensure they weren’t causing the loss. The softest dirt behind the pool is behind the weeping wall and in between the grattos. If the water is above the rock line it is seeping out of the pool.

I don’t know if they did any water proofing under the rocks. We would like to try to seal the mortar and rocks that sit in the pool, we just don’t know what product to use.

This is more than just water getting passed mortar joints on the stone. A steady stream is serious.

Is there a pipe that runs behind the waterfalls that may be cracked?

If you think it's at the stone line, the only true way I see to find and resolve the leaking, is to drop the water level below the stones and then remove them. Check for cracks in the structure.

Another method to locate the leaking is to perform a dye test. Anderson Manufacturing makes test plugs and also has a liquid dye in a syringe to allow for locating leaks in pool no matter if concrete, vinyl, etc.. You may try this prior to removing the stones in an effort to narrow down a suspected area of leaking.

It's possible there is a crack in the structure. Stone waterfalls cannot just be piled onto a typical pool wall. A structural engineer will design the pool to withstand and support the weight of boulders and stone for any waterfall. The wall thickness is designed accordingly.

Perhaps you could post some close up pics of the inside of the pool and also the backside where you see the water.

Here are a few more pictures. The pool was full on Saturday and now it is at the lowest skimmer line and the pumps won’t run because it is so low. I am going to give it a few more days to see if it continues to drain.