So I installed a huge 80ft round 6 foot deep pond/lake liner in my pond this summer. It has a slow trickle of a creek that feeds it. I filled the pond with water and its holding great. I have a small trickle of a creek that feeds it..but at the point of where the creek enters the pond is tricky. Ive built a little in-creek/pre-pond before is spills into the lined pond. That pond isnt lined. The pre-pond is always full...yet its not full ENOUGH to spill over into the lined pond. (It does when it rains). But WHERE is the trickle water going? I thought it might be going UNDER the liner...but it isnt. Ive felt around in there... Its not bubbling up. The weight of the water is holding it down. But WHERE is the water going? Very odd?
If I understand you right you're saying a trickle of water is going into the pre-pond but not raising the level of the pre-pond eough to overflow into the largerer lined pond --so it has to be going somewhere? Sounds to me like it's seeping down somewhere, whether it be the bottom of the pre-pond or seeping out sideways from the pre-pond and down.
You may have just enough seepage to keep the pre-pond water depth at equilibrium. All soils seep a little regardless of how much clay there is. Some just seep more than others. You could also have a sand vein or less impervious layer just under the bottom or sides of your pre-pond that the water is seeping into.
On my property I have so much clay in the soil you could make pottery out of it! However that doesn't mean there isn't a sand vein somwhere and I've seen them as small as a few inches in diameter.
With creek so close there is a good chance there is some silt, sand, gravel, etc. deposited by that creek that allows water to seep in.
Can you line the pre-pond?