What I found that works quite well for me is wiping out the container as best I can, then rinsing out with about a cup (depending on the size of the waterer) of half hot water and half vinegar. You may even be able to get away with this every other cleaning, since it seems to knock out a bunch of bacteria.
The plastic seems to be somewhat porous, so bacteria get started and just chow down on whatever little muddiness the ducklings leave in the waterer. It is a distinctive aroma, yes, indeedy!
An extra bit of disinfecting is to swish a little hydrogen peroxide around in the container after cleaning, then pour it out before refilling.