Rip-rap will discourage their tunneling.
What size rip rap should be used?
You've stumped me. when I order rip/rap they never give me a choice as to sizes? To me, rip/rap is pretty large, with chunks 6-9" long or so.
Just to clarify, are you wanting to remove existing 'rats, or prevent a new population from showing up? The reason I ask is due to you saying your water levels have been dropped. Muskrats will sometimes leave on their own accord when the water gets low and uncovers their runs and dens. Are you still seeing fresh sign?