I got an idea:
Try removing the pool for now and placing their water somewhere like this or in a depression in a corner -
photo from Duck Creek Farms
cover most of the top part of the run with a tarp to avoid the rain and place a ton of hay mixed with sand as the substrate.
With a pool...
do they stay in their pen 24/7 or do they free range too? Ducks are loyal free rangers and stick to their home territory. Maybe keep the pool and their water bowl away from their sleeping space.
try dry sand or dirt.
I raise all my baby birds outside after day 3 (with a heat lamp at their coop that they can return to when needed). I either use dried leaves or dirt as bedding. Now my birds rarely ever get sick at all, nor do they have any health problems. Even my little turkey poults...