I can attest to muddy waters and overpopulated crawdads. I did not believe that crawdads could stir up so much mud in my pond until I removed 150 (4-5 inch) crawdads form my pond this summer. Within a week after removal, the water in my 1/4 acre pond went from 12" clarity to 24". I used a clover leave trap baited with fish food in a sock. The best results were accomplished by putting the trap on the the bottom in about 1.5' to 2' of water, setting it at dusk and checking in the morning. More popular baits include chicken or dead fish, but fish food or dog/cat food in a sock has always worked well enough for me.

Disclaimer: I do not have the burrowing type of crawdads, mine are the northern Virile. You may have to set the traps more shallow...I don't know. I also have aeration im my pond that helped keep the crawdad stirrings from settling.

Plants that I have that the craws don't seem to kill off are...

Broadleaf Arrowhead,
Thalia Dealbata and,
Pickerel Weed.

I would bet that these plants will have trouble in a pond that the water levels fluctuate very much (more than a foot of depth).

One plant that I have seen on a few occasions that will follow the water level changes well is Smartweed. I have some around my pond that tends to live at the waters edge and can stand being in very shallow water for long periods, but I have also seen a variety of Smartweed that lives in waters up to a foot or so...this is the type you should look for. Some folks don't like it because it can make shore fishing difficult if the shore slope lends to shallow waters out further into the pond, but that is where it would benefit your situation...it might grow out into the water further and when the water drops, it would still be there and continue to grow out into the water as the ones further up the bank dry up, and vice-versa. The type I have around my place is fast growing and very hardy so long as moist soils are available.

The one thing you shouldn't have much of with abundant crawdads is FA. They eat it and keep the waters muddy so light can't get down to the bottom and grow the FA...point is, don't wipe them out, just cut them back a little at a time until you see good progress.

Fish on!,
Noel