Do you have a plan for the construction based on soils analyses, drainage, and topography?...or....are you using the contractor to assess the site(s) and provide options based on what he knows of the area for ponds?
I'm leaning on the contractors knowledge in this area. He's been in the business a long time. He hasn't visited the site yet, but will be in another month or so.
I'm curious what impact the leaves from the trees surrounding your pond has caused, if any?
