Sorry to hear you may be having some leaks in your new pond.
A pond sealed with clay-bearing materials should be mostly sealed immediately after construction. However, the clay minerals themselves do incorporate some actual water into their structure, so they will take up some of the free water from the pond and swell a little bit.
There is also some wicking, where the topsoil around your pond draws up some water above the pond level that is either used by your plants or gets evaporated from the soil surface.
You also will have some actual evaporation losses directly from your pond surface, especially on hot, windy days with low humidity.
After you take out all of that, then you may have a leak if you believe your water losses are greater than what I listed. Water or damp soil on the back side of the dam is usually a bad sign. However, as you said, some surface water can also run into that same low spot. You probably need to watch how that spot dries out for several days after a rain. If the other low spots on your property dry out in three days, and that one stays wet for 10 days, then you probably have a pond leak.
If that is the case, you should probably come back to the forum and start a new thread. You can then post more info about your pond situation and people can help you with possible solutions.
Good luck with your new pond!
