I had been losing up to 1 inch of water every day during the summer. I tried fixing all the usual problems of liner folds, ground water, splash out, and pipe leaks. Then I did two things differently and the water loss is now less than 1/4 inch per day which could be natural evaporation and plant expiration.
1) I pulled back the hyacinth in my veggie filter a few inches from the edge of the filter at the water fall. This reduced the height of the water in the filter by 1/2 inch. Apparently the thick roots were damming up the flow which would allow water to be siphoned off through liner folds.
2) I fed some of the hyacinth to the koi. As they ate the hyacinth its plant parts were shredded and some parts even became a gelatinous film. I suspect that some of this plant material migrated to an unknown hole and is plugging it. I know it stopped up my leaf basket fairly well. I can only hope that this natural patch will continue to prevent the leak. If you don’t have fish to shred your hyacinth, put it in a blender with some pond water and dump it back in the pond. I had once read you could do the same by adding cat litter. Supposedly the cat litter will migrate to a leak point and swell and become hard over time. I wouldn’t recommend cat litter in a koi pond but it may work for a water garden without fish.
3 – maybe) In doing recent pipe changes I noticed the bio film on the pipes was much greater than previous cuts. It could also be that bacteria are plugging some of the piping’s minute leaks. Cooler temperatures may be playing a role here too as the pipes and fittings can shrink.
I can’t guarantee this will work for you. Here is a link to one of may earlier articles for other causes you may want to explore: Water Loss – Where does it go?