That boat looks so lonely out there so far from the water.

My guess is that you must have a decent watershed to fill up that much with 2.5" of rain and/or your pond is a water table pond and the water table rose up that much with the rain event. And, I don't think those trees are your biggest problem with water loss. I'd wager your pond is leaking and/or you don't get enough rain to keep up with evaporation. Not that big of a deal if you are going to redo it. Just redo it right and the new and improved version won't leak. The info for redoing it right can be found here, but I will leave that to the experts.

Fish on!,
Noel