The Monument is located near the San Andreas Fault, which had a hand in creating the unique formations the Monument protects. The Pinnacles are part of the Neenach Volcano which erupted 23 million years ago near what is Lancaster, California today. The movement of the Pacific Plate along the San Andreas Fault split a section of rock off from the main body of the volcano and moved it 195 miles (314 km) to the northwest. It is believed that the pinnacles came from this particular volcano due to the unique breccias that are only found elsewhere in the Neenach Volcano formations. Differential erosion and weathering of the exposed rock created the Pinnacles that are seen today.
Large scale earth movement also created the talus caves that can be found in the Monument. Deep, narrow gorges and shear fractures were transformed into caves by large chunks of rock falling from above and wedging into the cracks leaving an open area below.
Since the Pinnacles were moved to this area, the San Andreas Fault has shifted 4 miles (6.4 km) to the East of the Monument. The original location of the San Andreas can be seen in the Chalone Creek Fault. Two other large faults are known to run through the Monument, the Miner's Gulch and Pinnacles Faults. These faults parallel the San Andreas and were most likely caused by major movements of the main fault.
Seismic activity is frequent in the Monument and United States Geological Survey maintains two seismometers within the boundaries. Evidence of past and ongoing seismic activity can be seen in offset streams where they cross faults. Valley bottoms and terraces show signs of uplift.
Prairie Falcons breed in this area in some of the highest densities of anywhere in North America. Peregrine falcons have recently returned to the Monument to breed also, but in far fewer numbers. A California Condor re-establishment program has been in place since 2003. Bobcats, mountain lions, coyotes, California Quail, Wild Turkeys, and many other birds and mammals live in the area. Like many parks in central California, Pinnacles has had a small problem with wild pigs (a mix of feral domestic pigs and imported wild boars) disturbing the landscape on a regular basis. As of Spring 2006, the core of the park was pig free. The culmination of a twenty-year, 1.6 million dollar effort had succeeded in eradicating pigs from the main area of the park. National Park Service personnel along with IWS worked to remove pigs from inside the park, and establish and monitor an exclusionary pig fence that runs for approximately 26 miles around the center core of the park. Outside this fence however, wild pigs still roam in regular abundance in and around the federally maintained campground within the east side of park. Such is the pervasiveness of the problem. Current monitoring for potential breaks and breaches in the fence is needed to ensure that the pigs do not return to devastate the park.