So you are asking how to make a muddy creek not muddy?
I've heard of mud walking shoes, that are like snow shoes but for mud (I think there is a patent on this even) you could put on over waders. That might work, but I'm not sure how well they work. If it's real muddy, and your mud/snow shoes get below the surface of the mud, you might have problems.
Maybe you could take a weedeater with a brush end on it, and cut yourself a nice path along the creek bank where it isn't muddy, but still at a lower elevation than the surrounding area, and not actually walk in the creek.
Or....
Pray for a wet year so you can float a kayak/canoe.
Rent an excavator and dig it out so you can float a kayak/canoe.
Or get a few truck loads of rock instead of a few pocket fulls, put it in the creek, and then think of better things you could have done with your time or money.
Or do nothing and thank yourself for not pissing your time or money away trying to make a muddy creek not muddy?
Good luck!