FR,
Knowing you are in tall grass prairie country, you may be surprised at just how much organic matter and nutrients are in the topsoil. Sounds like you may have a hard pan underlying. To me its all good. However be careful of have much topsoil remains in the pond. Organic percent greater than 3% is borderline hyper-eutrophic and any shallow areas inundated that have that level or greater organic matter content will grow vegetation prolifically.