The source of Deep Creek is at an elevation of , at the head of
Little Green Valley in the
San Bernardino Mountains. It initially flows southwest, through the communities of
Arrowbear and
Running Springs, before turning north. It is joined by Hooks Creek from the west; a dam on Little Bear Creek, a tributary of Hooks Creek, forms
Lake Arrowhead. A short distance downstream is Aztec Falls, a popular swimming area at a waterfall along Deep Creek. The creek continues north, at the bottom of a deep gorge through mountainous wilderness, receiving Holcomb Creek and Coxey Creek from the right before turning west, forming a canyon between the San Bernardino Mountains and
Ord Mountains. The
Deep Creek Hot Springs are located along the stream where it turns to the west. The
Pacific Crest Trail follows the Deep Creek canyon for , from the confluence of Hooks Creek to the mouth. Deep Creek ends at its confluence with the
West Fork Mojave River forming the Mojave River, at an elevation of . The confluence is located southeast of
Hesperia, directly behind
Mojave Forks Dam, a flood-control structure built in 1974. ==Drainage basin==