I don’t know about rock lining, but in my little 1 ac pond I got rid of muskrats (33 only last year) with a simple raccoon trap (bought on amazon) and apples.
I set the cage near the shore with half apple inside and the other half cut in 5 or 6 pieces in front of the trap. Burlap and some branches covering it. Every morning I found a muskrat in, till I got all them.
