It's going to depend on how you set it up and manage it. There will be a bit of mess especially close to the kiddie pool due to splash.
Some things you can do to manage:
Make sure the drainage works well all the time. I underestimated the amount of slope I would need to keep the muddy water from puddling in one part of the duck pen, and it did not become apparent for nearly nine months. After that much time, the plant fibers from foraged plants and loose straw gummed up what I had, and it became anaerobic. No major gag-me stink, just a little whiff of swamp, and I made some changes. Took me about three hours to fix it up and now the used water pours off into the channel to the grape arbor again.
Holderread recommends a platform covered with something like half inch hardware cloth (I'd use coated wire), or instead of a platform, a few inches of pea gravel. I use pea gravel, but it got gummed up so I needed to create more of a slope, which was pretty easy.
Harness the inevitable: my runners - much smaller than muscovies, but I have ten and you have two
have very moist droppings. I add straw, oak leaves (really help keep odors down), coir, and other high-carbon materials that absorb moisture, attract worms which the ducks eat, and produce some fabulous compost for my garden.
I have heard of chickens drowning, but I don't know how common that is. Just a thought. Ducks need water to bathe in as well as drink, so having it available to them is critical. Having their own water supply helps the chickens, too, I am told, since ducks muddy up water within minutes - sometimes seconds after it is cleaned and refilled.
Some people plumb their pools and drain the water into a field or garden area (great nutrient!). Making sure the pipes are sized correctly to avoid plugging up is part of the exercise. I just dump the concrete mixing pan into the channel and it goes downhill to the grape arbor. Simple. Easy to fix up if a straw dam forms.
Those are my initial thoughts. Muscovies are fascinating animals. I am happier with my small breed, but I think you will enjoy your new babies.