The creek begins on the eastern slopes of the
Wasatch Plateau at elevations above . It turns southward near the town of
Emery, then southeastward, where it crosses under
Interstate 70. It then enters the western flank of the
San Rafael Swell and, continuing southeast, it passes Hondu Arch and the Tomsich Butte mining area before beginning its spectacular passage through a narrow
slot canyon of
Coconino Sandstone known as “the Chute". After merging with Chimney Canyon and passing the Hidden Splendor Mine area, it passes through the southeastern escarpment of the
San Rafael Reef at the end of Muddy Creek Gorge. In its lower reaches, it continues southeastward through the Blue Hills
badlands near Caineville, then cuts through the Jurassic
Morrison Formation where
dinosaur fossils have been found. Finally, after an estimated length of and a drop of , it meets the
Fremont River some miles north of the town of
Hanksville where the two form the
Dirty Devil River (which then flows south to meet the
Colorado River). Since it enters the San Rafael Swell at an elevation well below that attained by the Swell itself and continues through the Swell's entire expanse, Muddy Creek is a very ancient river course, "superimposed" on the entire San Rafael uplift and therefore predating the time when the latter arose some 60-40 million years ago. ==Wilderness==