If you've got runs going into the bank, you can use Conibear 110's to catch them one at a time, or get some "colony" muskrat traps. They are wire box traps that have a door on each side. Make sure they are completely under the water when set, and any caught will drown. I've caught so many in one trap that I had to really work to get the door open to get them out. You can clean out a den in a hurry with them. Get enough to cover all the den entrances in your pond and I'll bet you could clean them all out in 2 days max.

You can build your own too....

http://www.gbso.net/actor/building_a_folding_colony_trap.htm

www.hoosierpondpros.com

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3/4 to 1 1/4 ac pond LMB, SMB, PS, BG, RES, CC, YP, Bardello BG, (RBT & Blue Tilapia - seasonal).