Setting den entrances with body grip traps work great in these locations, as well as colony traps (box traps) in the "runs" leading to the holes. Depending on the depth of the water, hipboots or waders may be needed to find these entrances with your foot, while wading. Often, these holes and runs are a few feet from the bank. Another consideration, is sign trapping them, which is making mud slides from the waters edge, up the bank. These are made about 4" wide, and run up the bank a couple feet or so. I prefer 1 1/2" longsprings, but coils can be used. These are staked with a tally pole, to deeper water, and the trap is bedded at the base of the slide, just under water. Muskrats swimming by will quickly be drawn to these mud slides, and approach them at the base, where your trap is set. After caught, the weight of the traps will quickly drown them, given there is a foot or 2 of water where staked. Now, having said that, if otter or beaver occupy this same stretch of creek, you may want to avoid the "sign" trapping, and stick with the first mentioned.
Float sets may be an option too.
(Check local laws on whether or not colony traps are legal to use)