We've brooded ducklings twice now, and are starting to get the hang of it.
The first time we tried to brood ducklings the same way as chicks. (I suppose everyone tries that.... ONCE!)
Now we still use a Rubbermaid chick brooder with "agricultural quality" towels for the first week, then move them outside to a 5' diameter stock tank brooder with lots of pine shavings.
The pine shavings by the waterer do get wet, but we just stir wet and dry shavings together with a rake. (Works great in a desert climate, maybe not so great in more humid climates???) The brooder lamp helps dry the bedding out as well, even when the ducklings don't need it for warmth any longer.
Then about every week we add fresh shavings, kind of like the deep litter method, until about the fifth or sixth week when the ducklings are moved to a 10' x 10' straw bale enclosure with straw on the floor, and the waterer is placed on a screen on top of a tub, to keep the mess to a minimum. ("Minimum" being relative, of course.)
Bryan