When I did the C&O, I noticed little puddles, even on elevated sections where one would have expected them to drain. I am not a soil scientist, but I suspect that there is a lot of impermeable clay in the surface. They would have used clay to line the canal. If the NPS is maintaining historical integrity by using clay on the towpath (now, walking and biking path) it will always be muddy.
One thing we can do to help them and ourselves is to lubricate the hiker biker pumps that access that delicious iodinated water. A little Trip-Flow helps the water flow.