I would be very curious to get the soil tested just under the muck line. I have seen a few folks on here who have renovated a pond like this but had problems with clarity and algae blooms after it filled back up. I am wondering if a high degree of nutrients leaches out of the muck into the subsoil being exposed, and if so, how to remedy that nutrient load so it doesn't return to the water too fast. Now would be the opportunity to check it out.

If high in nutrients, perhaps line the pond with a fresh layer of clay before filling? Perhaps dig a little lower and see if there is less down below?