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I have a nice timber hole in southern Illinois that we flood right before the season starts. e have it planted in millet in the summer and a levee system that we can control the water . A good high output pump to flood it about a week prior to opener.
This year we could not keep th water where we wanted it and after some investigation found a couple of spots where the muskrats had burrowed thru the levee. I finally put about 300 lbs of bentonite around the holes and with a little work got the holes stopped up but we lost 1/2 the season.
Anyone have experience or a suggestion on this so we can get in front of it next year?

kill them

Can you hire a trapper for that job ?

trade the muskrats for a pair o' beaver

Hire a trapper if you have the means, best money you will spend. Otherwise, there are several ways to handle them, they are pretty stupid. They love carrots (seriously), bait them up adn shoot at night. There are also pleanty os sites on the web that show you how to build floating traps for them. But again, trapping by a pro will be most effficient.