Put the waterers up so they can still get their heads in, but not their bodies to climb in. Using the chick waterer, I never really had them pooping in the water dish. It was always full of food, but not poop.
I have a large rubbermaid type shallow bin outside for their water. They can get in it, and do, but only when their pool is disgusting and then it is usually just Cadbury that hops in for a quick bath.
I have their food in a square storage bin, also on the shallow side. They can also get in there and sometimes do, but typically they just stand on the outside and eat like good little ducklets.
Ducks just poop. So if you don't want poop in something, you'll have to figure out how to get it out of pooping range. Get it up and block off access to their back ends.