The best way to prevent muskrat invasion is to design muskrat-unfriendly structures by constructing farm pond dams to certain suggested specifications. (Dam specifications can be found at the link below). For existing structures, modify existing habitat and eliminate aquatic or other foods favored by muskrats. If farm pond dams or levees are being damaged, one way that damage can be reduced is to draw the pond down at least 2 feet (61 cm) below normal levels during winter. Then locate and fill all dens, burrows, and runs, and rip-rap the dam with stone. Once the water is drawn down, trap or otherwise remove all muskrats.
Resources: (online)
Muskrats
