Muskrats can become a destructive nuisance in ponds. The most effective way to deal with a muskrat problem is trapping. Remember that muskrats are rodents and share similar characteristics with their smaller brethren (rats and mice) including a very high reproductive rate. A couple of muskrats now can mean many of them in a short time.
These traps are humane and easy to use. Set traps in observed muskrat runs and den entrances. Body grip traps should always be set in the water to avoid catching animals other than muskrats.
Thoughts on Live Traps — some people prefer the idea of live trapping these animals and releasing them somewhere else. Remember that you are trapping them because they have become a destructive problem; releasing these animals at another location is likely to simply give your problem to someone else and may be illegal!