The water hits some underlying underground rock and fills. It seeps in through local cracks in the rock.
The water seeping in through the cracks in the rocks WITHOUT any water flowing along the surface is the very definition of a "groundwater pond".
You cannot seal the cracks to save the water, because that is how the water usually enters your rocky pool.
The good news is that your shallow, rocky pool might be connected to a very large aquifer. Have you been able to use the irrigation pump for your orchard for several weeks without significantly lowering the water level in your pool?
If so, do you have any non-rocky ground near the orchard where you can build a pond? I am asking, because it might be possible to pump water at a low rate from your rocky pool into a newly constructed pond. That would give you a water supply that could still be used when the groundwater level in your pool recedes with the seasonal drying.
If you have sealing clay, you want your new pond to be as deep as feasible to store the most water while minimizing surface evaporation losses.
Good luck with your orchard!
