Another thing would be to take a wide shallow pan or tub and fill it with water, placing it near the pond. You can use that to check evaporation rates. You might be seeing waer evaporating away, or if there are any trees near the pond they could be sucking up the water as well.

How did you compact the soil (clay) in the upper 5' or so of pond depth? How thick is the clay that you compacted in that area?

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3/4 to 1 1/4 ac pond LMB, SMB, PS, BG, RES, CC, YP, Bardello BG, (RBT & Blue Tilapia - seasonal).