The duck is made of atoms that exert a gravitational force on all other objects and attracts them slightly. The earth is also made of atoms, so it also exerts a gravitation force on all other objects, but it's much larger so the gravitational force is much stronger so it's much more attractive. That means from our perspective on the earth, the duck is effectively pulled down, thus putting a downward force on anything that might be directly beneath it.
This remains true even if the duck is sitting in water. That said, the water is likely significantly heavier than the duck in general, so the change in weight will often not be noticeable, however it will be there.
There is a way where you can make the duck not have a weight on the scale, and that is to turn the whole system upside down and put the duck on the floor, and then the water, then the scale on top face down. If you do this then you won't be able to read the scale anymore because it's upside down you fucking retard, and you spilled water all over the fucking floor you literal spastic. Have you ever used a scale?
On the plus side, you are at least more attractive than a rubber duck, gravitationally speaking anyway. So enjoy that fact and have a nice night.