The basin contains the communities of Yucca Valley, Twentynine Palms, Joshua Tree, Pioneertown, Morongo Valley. The southern edge of the basin includes the Joshua Tree National Park. The northern boundary encompasses the Twentynine Palms Marine Base.

The drainage basin stretches approximately from the Little San Bernardino Mountains north of Interstate 10 in the south, to the Interstate 40 area in the north. Lying within the Mojave Desert, the Morongo Basin is east of the city of San Bernardino and San Bernardino Mountains, and north of the Coachella Valley and Colorado Desert.

The Morongo Basin is located within the Mojave Desert and in the High Desert region of Southern California. The area's elevation can range from 1,950 feet (590 m) in Twentynine Palms, to 3,000 feet (910 m) in Yucca Valley.[citation needed] The higher sections of Joshua Tree National Park are within the basin.

The terrain in the area is a desert landscape of hills and alluvial fans framed by mountain ranges.