Is the part of the yard that floods dirt or rock? I'm thinking if it's a natural waterway you could just leave it and let the ducks have fun when it floods. If it's a wet mess anyway I'm wondering if the ducks would do much more damage then the flood waters. You could always let them on it and see how it goes. If that won't work, maybe you could put up temporary fencing when it floods.
You might think about setting up their new pen with something other than grass. In my run I have part pea gravel and part deep litter. I have to say in warm weather I prefer the pea gravel because I just have to spray it down with the hose. In the really cold weather it freezes and is hard to clean. But I have to keep it because it does work really well for draining away the water from their pond. I do like the deep litter though. It doesn't take much work to keep it from smelling and it doesn't take much litter (I use pine shavings and straw). I have also read that some use artificial turf and it works pretty well. But I image that's expensive. Wood mulch is another option.
I don't image culling will be easy. It shouldn't be. Cymbaline makes a good point. You could wait till spring and see which males are the more aggressive breeders and cull them. You could also separate the males from the females during the breeding season. If you want fertile eggs you could just leave one or two with the females. You could also look and see if you can find some more females.
You might think about setting up their new pen with something other than grass. In my run I have part pea gravel and part deep litter. I have to say in warm weather I prefer the pea gravel because I just have to spray it down with the hose. In the really cold weather it freezes and is hard to clean. But I have to keep it because it does work really well for draining away the water from their pond. I do like the deep litter though. It doesn't take much work to keep it from smelling and it doesn't take much litter (I use pine shavings and straw). I have also read that some use artificial turf and it works pretty well. But I image that's expensive. Wood mulch is another option.
I don't image culling will be easy. It shouldn't be. Cymbaline makes a good point. You could wait till spring and see which males are the more aggressive breeders and cull them. You could also separate the males from the females during the breeding season. If you want fertile eggs you could just leave one or two with the females. You could also look and see if you can find some more females.