WOW. Really jumped in with both feet. I have a few ducks, its just my wife and I, we like the eggs, and the occasional one for the table. Our current "pond" is hardly more than a puddle. Just dug a MUCH larger pond, but it needs a liner or a lot of bentonite before it will hold water more than temporarily.
Will offer what experience I can, and look forward to seeing your future postings. That's quite the journey you have begun!
Snapping turtles definitely pose a serious problem to waterfowl. There are several things you can do to decrease the risk of them injuring, or possibly killing your ducks, but it will be hard/ almost impossible to totally reduce the risk of them getting injured.
I have around forty ducks and a few geese, and I also have a few creeks and a pond that they use. To control the snapping turtles around here I trap on a regular basis, using a steel turtle trap, which basically has the same mechanisms, and design as your normal raccoon trap, but is wider to allow easier access for the turtle. I stuff an onion mesh bag with organs, and tie it to the back of trap, and set it out each night. If you do it during the day you'll have a duck in the trap. There are other ways of trapping them, but I've found this way to be fairly easy, and doesn't take too much of my time up out of the day to do.