Another option would be to build a designated duck pond.

You are going to have lots of spoils (dirt) from excavating for a 3-acre pond. Once you get down to clay, you could move that material to one side and make a small pond on high ground that was only 1-1.5 feet deep. Seed it with rice and millet and then flood it in the fall and the ducks will think they are in duck heaven. Maybe dig one deep hole in the middle so your "duck pond" will have open water for them to land.

You would have to pump water up to that pond, unless you could design it to capture water from your watershed. In that case, it could act as a silt trap for your main pond.

If you did intend to keep it full most of the year, you could install a bottom drain and a deeper "easy seine" area and grow some forage fish in that pond. When the forage is the right size, slowly decrease the water level to concentrate the fish, and then seine a bunch and move them to your main pond.

Just throwing out more ideas while you are still in the design phase of your big project!