I struggled with this for a long time, the ducks were muddying up every water source in sight and causing my chickens to become ill. I would say you have two options;
Converting to nipple style watering systems for your chickens and providing a pool or bowl for your ducks. This prevents the ducks from emptying and soiling every water source available. You can purchase kits or pre-made nipple watering systems over the internet for relatively inexspensive.
The method I use however prevents you from needing to go out and purchase an entire new set of watering systems. It came to my attention that ducks do not fly or perch well unless you have muscovys. So I set up a system that raises my 5 gallon basin waterer off the ground high enough so the ducks cannot reach it, but low enough for the chickens to jump up and land on the platform and drink. For the ducks I provide a kiddie pool on the ground, sometimes the chickens still drink from it, but at least they have the option of a cleaner source of water.
