Beginning about 60 million years ago, the Colorado Plateau, of which the park is part, was pushed upward by tectonic forces and exposed to increased erosion.

[17] Petrified Forest National Park is known for its fossils, especially of fallen trees that lived in the Late Triassic Epoch of the Mesozoic era, about 225–207 million years ago.

Streams flowing across the plain from the highlands deposited inorganic sediment and organic matter, including trees as well as other plants and animals that had entered or fallen into the water.

[18] The colorful Chinle, which appears on the surface in many parts of the southwestern United States and from which the Painted Desert gets its name, is up to 800 feet (240 m) thick in the park.

[19] It consists of a variety of sedimentary rocks including beds of soft, fine-grained mudstone, siltstone, and claystone—much of which is bentonite—as well as harder sandstone and conglomerate, and limestone.

[18][19] Exposed to wind and water, the Chinle usually erodes differentially into badlands made up of cliffs, gullies, mesas, buttes, and rounded hills.

[18] About 60 million years ago, tectonic movements of the Earth's crust began to uplift the Colorado Plateau, of which the Painted Desert is part.

Groundwater dissolved silica (silicon dioxide) from the ash and carried it into the logs, where it formed quartz crystals that gradually replaced the organic matter.

However, a small fraction of the logs and most of the park's petrified animal bones have cells and other spaces that are mineral-filled but still retain much of their original organic structure.

Other organic matter—typically leaves, seeds, pine-cones, pollen grains, spores, small stems, and fish, insect, and animal remains—have been preserved in the park as compression fossils, flattened by the weight of the sediments above until only a thin film remains in the rock.

Among the groups represented are early theropod dinosaurs,[23][24] crocodile-line archosaurs,[25][26][27][28][29][30] temnospondyl amphibians,[31][32][33] lissamphibians,[34][35] non-archosauromorph diapsids,[36][37] and other dinosauromorphs[38][39] and archosauromorphs.

According to the United States Department of Agriculture, the plant hardiness zone at the Painted Desert Visitor Center 5,764 feet (1,757 m) is 7a with an average annual extreme minimum temperature of 3.1 °F (−16.1 °C).

Between 8000 and 1000 BCE, the Archaic Period, nomadic groups established seasonal camps in the Petrified Forest from which they hunted game such as rabbits, pronghorn antelope, and deer and harvested seeds from Indian ricegrass and other wild plants.

[62] During the Basketmaker III period, 500–700 CE, families occupied shallow subterranean pit structures, at first on mesas or other vantage points and later at the base of bluffs and in lowlands, where the soil was better.

Similar to much of the Ancestral Pueblo world, population density increased rapidly at this time and nearly 1,000 sites dating to this period have been identified in the park at a wide variety of locations—at the mouths of washes, near seeps, and on moisture-holding sand dunes.

U.S. Route 66, a former transcontinental auto highway developed in 1926 from part of the National Old Trails Road, ran parallel to the railroad tracks until it was decommissioned in 1985.

Between 1934 and 1942, the federal Civilian Conservation Corps built road, trails, and structures in the monument, and the government acquired additional land in the Painted Desert section.

Despite a guard force of seven National Park Service rangers, fences, warning signs, and the threat of a $325 fine, an estimated 12 short tons (11,000 kg) of the fossil wood is stolen from the Petrified Forest every year.

[69] Professional archeological work in the park began in the early 20th century when Walter Hough conducted excavations at Puerco Ruin and other sites.

[23][4] In 1921, Annie Alexander, founder of the museum, visited Blue Mesa to collect more of the phytosaur and other specimens; this led to further excavations by paleontologist Charles Camp.

[4] Camp was the most prolific collector in the early 20th century, but collections were also made by Maurice Mehl (University of Missouri), Edwin Colbert (American Museum of Natural History), and park naturalists like Myrl Walker.

[72] In the northern part of the park, the volcanic soils of the Bidahochi Formation support abundant plant life along the Painted Desert rim.

Growing among the grasses are flowering species such as evening primrose, mariposa lily, and blue flax, and shrubs such as sagebrush, saltbush, and rabbitbrush.

Here the invasive Eurasian tamarisk, also known as saltcedar, threatens native plants by crowding, using most of the available water, and increasing soil salinity by exuding salt through its leaves.

[72] Some of the larger animals roaming the grasslands include pronghorns, black-tailed jackrabbits (hares), Gunnison's prairie dogs, coyotes, bobcats and foxes.

[73] On the Painted Desert rim, small animals find food and shelter among the denser foliage, and mule deer sometimes frequent the area.

More than 16 kinds of lizards and snakes live in various habitats in the park and consume large quantities of insects, spiders, scorpions, other reptiles, and small mammals.

[76] Raptors, songbirds, and ground birds are found in the park's grassland, while the Puerco River's riparian corridor is a good place for year-round residents as well as migrants such as warblers, vireos, avocets, and killdeer.

The Rainbow Forest Museum complex 2 miles (3.2 km) north of the park's south entrance offers services including information and "Timeless Impressions" showings once every half-hour.

It has a bookstore, fossil exhibits, an interactive Triassic Virtual Tour, limited food service, a gift shop, and public restrooms.