Rob,

There are probably better ways and muskrats may be different, but in rennovating an old pond recently we found a couple of nutria (the southern water rat)dens a little over a foot below the water line. Finding these holes explained why the old pond never held water above a certain level. Just packed the holes with clay with the dozer and everything is fine now. It would not be very expensive, if all you need to do is plug those holes, to just lower your water level and pack in the clay. A dozer could do that in no time and you probably could even do it by hand with some difficulty. The nice thing about the dozer is that you can cut into the hole area and really pack the clay in good.