Duckling whistling while he breathes
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Do they have water deep enough to dunk their heads and clear out their nares? It is possible the duckling has dried food stuck in the nares? That can cause a whistling sound and heavy breathing. If it's just that it can be fixed by just giving them a lukewarm bath so they can really clear out their nares, then also providing them deep enough water to clear out their nares at all times in the brooder. (You'll want to make sure they are not able to get more than just their face into the water, though. You don't want them to get themselves and the brooder all wet and get chilled.)
If that is not the issue, the duckling may have a respiratory infection, which will require antibiotics.