I have a lake in the back yard and a muskrat infestation a few years back. Started to trap them when I noticed two submerged holes along the bank bordering the lake.
I used a pair of box traps (4"-6") and placed them right at the opening of the holes, un-baited. I checked them in the morning and evening and in the first year I took out 38 of the critters from those two holes. The second year I got 24 before the bank started caving in. Even got a catfish once, but I practiced catch and release on him.
I had to rebuild the bank and rip-rap the shoreline to finally get rid of those pests.