Your garden pond is very nice...Makes me want one.
The splashing of the water fall will contribute a lot to evaporation. The surrounding rocks are getting wet and are warm. Most of the water that hits the rocks may be evaporating. This speeds up the water loss.
This is what I'd do...turn off the fountain pump and the other pump for a day (maybe two). Put a five gallon bucket of water next to the pond (no lid) and mark the levels of the water in both the pond and the bucket. Loss due to evaporation should be very close to the same in both. If the bucket loses a 1/2" of water, so should the garden pond...for example. If the pond loses a lot more without the pumps going, then it's probably leaking. A rain event would nullify the test and depending on temperature and humidity, it may take a couple days to see measurable amounts of water loss.
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