Your pond is really cool. How old is the pond and how much has it silted in over the years? That recent picture of the lower water before the recent rain makes it look like some silt has been pushed into the pond from the creek.
My neighbor built a pond by building a dam across a valley that has a seasonal creek in it. It is pretty crazy to see how much silt and sand has filled in his small pond in the last few years, but that is a tiny 1/4 acre pond so a little silt/sand makes a pretty noticeable difference.