When you are looking for dens/runs, pay close attention to the dam. If you do have a 'rat population, I'd check with the DNR and see what you need to do to cut the population nunbers down legally. Even tho you can use the SSS method, you really don't need the boy's (and girl's) in green asking questions. They can multiply pretty rapidly, and make a mess of the banks and dam. With fur prices down over the past years, there isn't a lot of incentives for trappers to be out, so the excess population needs new homes, and the habitat that you are creating is calling. Nature abhors a void. The next thing you'll see is a mink, which prey on the 'rats, but it won't be enough to keep the population in check.
If you look close at the first pic, to the right of the dirt in the water, and to the left of the grass, it looks like a 'rat run going to the caved in area. If you had hip waders on, you can walk in the water and stick your toe in that area. If you can feel a semi-circular trench going up under the bank of the pond, you can be assured that it was made by a muskrat. They don't tunnel or make runs in deep water, the deepest that I've seen them around here is in 2' of water.
Beaver on the other hand, will make runs much deeper. I trapped a 70# one at a duck club in Plainfield years ago that had a run in waist deep water, and the bottom of the run was deeper than my chest waders. The 330 caught him right behind the ears and the trap hardly moved. That's when I really started to respect the power that's in the 330's.