Scout and Nubtush:
Coming from a trapper, there are a lot of ways to get ride of the target animal in question. Before starting, first I would ensure local game laws are followed. In Michigan, we can take certain animals on private land during any time of year if they are "doing, or about to do damage". You simply need a license of any kind.
Raccoons love waterways. They search all the time in the shallows for shellfish. Crawfish, clams, and small snails to name a few. Without getting in to way to much detail or highly intricate trapping techniques, the simplest way to trap raccoons is with the use of a DP (Dog Proof) trap. You can do a search for them and see how easy they are to use. Most importantly, you will not catch non target animals (such as dogs or cats) in them. Once set, you pour bait in the tube (next to water I would use some sort of shellfish bait, clams, tuna fish) and then a call lure. Once caught, they don't necessarily harm the animal and they can be released (if wanted) without damage. In Michigan, you cannot transport live animals from private land to release on public land. Dispatching them with a 22 is best. You can also use drowning rigs, but that is more than is needed.
As for Muskrats.... They are a hug pain when it comes to tunnels. Two ways to do it. One, you can contact a local trapper in the area and allow him to come and trap the animals (during season) when the pelts are prime. You take care of your issue, and they get to keep the pelts, carcasses and so on. If not: 110 and 120 conibear traps set in front of their tunnels do the job. It is a kill type trap that will snap their necks in pretty short order. Only downfall to this is you will only get one at a time. Their are several ways to trap muskrats. All have pros and cons. A float style rig with Duke #1's work really well and you can catch multiples off the same float. Another option is a colony trap set down in a water passage. Again, multiple catches can be had at the same time. Google colony trapping for muskrat, float trapping, or just muskrat trapping in general to get a better idea of the examples.
I have OCD "Obsessive Crappie Disorder"