Very late post to this quesry.
I have chix and muscovies in the same area with no problem. They mostly ignore each other. For some reason this winter for hte first time ever three female ducks have taken to getting into the chicken house at night. It is raised on stilts. Rain, snow, etc., really doesn't bother them, so this is a little perplexing.
In terms of water, the ducks will turn clean water filthy in a heartbeat- it is amazing how fast they can do it! I am convinced with the muscovies a lot of what I see in the water is actually food. They are probably really filter feeders- their beaks have little serrations that they sieve water through once they've taken a bite of food- which would explain why there appears to be a layer of food on the bottom of the water container, which is a kiddy pool in the summer.
This is, of course, a huge waste of water, since I don't feel like taking it out bucket by bucket to water and nitrogen-enrich different parts of the garden daily... there are a couple of YouTubes on "Duckoponic" systems, where you run the dirty water through beds with plants the ducks will eventually eat, then cycle it back as clean water for the ducks. THat is my goal for next summer.