Is the black balloon thing on the bottom of the pond in one pic a pump? I might put the pump on a platform (eg a big upturned plant pot with a cement paver on top to hold it down) so it doesn't just draw up sludge from the bottom. I might also use a sump pump designed for dirty water rather than a pond pump (if you haven't bought the pump already). A sump pump is tough and can handle mucky water better than a pond pump.
Plans for the duck hut look great. They only need something very simple. Just monitor how hot the metal roof gets in summer. If it it radiating too much heat downwards into the hut then you can put a layer of timber under the metal to insulate it a bit.
How high is your fence and are you going to make a digging barrier at the bottom to keep predators away?