Although most domestic breeds of ducks have lost their ability to fly there are exceptions: Muscovies, Calls, East Indies and domesticated Mallards can all fly to some extent so if you keep any of these it is a good idea to clip their wings. This is quite straightforward to do by simply trimming the primary feathers on one wing. Clipping one wing will unbalance the duck making flying impossible and is completely painless, in fact to the duck it is a bit like having its hair cut.
Only trim the primary feathers as the others are important for insulation. With a lightly coloured duck you can see where to trim the feathers by holding the wing up to the light. You will see where the bloodvessels start in the shafts of the feathers. Finally, don't forget to clip the wings again each time the duck moults!
Please note that if you are in doubt about how to do this please consult your local vet.