Brandi, I love your little pond and can't believe it is filling from the bottom up. Your water table must be very shallow to get that kind of seepage. Consider this, though. You are saying that it's all clay, but there is water coming in. If the pond is clay that would seal water from running out, wouldn't it seal water from running in? I'm thinking that if the pond fills up from rain, the level will quickly adjust to whatever the water table is for the season.
I love that clear blue water you are getting into your pond. Actually, I'm really jealous of it.

I just think that it indicates a seepage, and whatever level your water rises to from that seepage will be the average costant level of the pond year round. If it comes up another 18" it won't matter anyhow. You'll have great little clear pond in which you can count every fish.