The world's geology has been and is still created in many different ways. There is constant shifting along fault lines, plates collide creating mountains and valleys, and volcanoes erupt creating land where once there wasn't any. The Earth's climates change as well due to its wobble on the axis and its relationship to the Sun's warmth. Climate affects geology in many ways by freezing, thawing, eroding, and depositing landscapes by way of wind and precipitation. Glaciers can freeze and thaw affecting the depth of the oceans and the land that it covers. Except for catastrophic events such as volcanoes, floods and earthquakes, much of the earth's geology has been created at an imperceptibly slow pace. Millions of years are often required to produce the landscapes we see today throughout the world.

Tallgrass Prairie National Preserve is located in the heart of the Flint Hills region of Kansas. This physiographic region extends from the Nebraska border southward into northern Oklahoma, and is from 30 to 100 miles wide. The hills are usually flat-topped with concave slopes that have developed on the underlying limestone and shale layers. These limestone and shale sediments seen in the Flint Hills today show us a cross section of a landscape that looked much different long ago.

The geologic time period represented in the Flint Hills is referred to as the Permian Period of the Paleozoic Era, which was approximately 250-290 million years ago. The Kansas of today was a bed of a vast shallow body of water called the Permian Sea. During this extensive time period the earth's oceans rose and fell many times creating different types of aquatic environments. The shallow warm seas supported enormous numbers of invertebrates, fishes, and amphibians. Many animals and plants (such as oysters, corals, some sponges, sea urchins, plankton, and algae) take calcium carbonate (CaCO3) out of the water and secrete it to form shells or skeletons. As these organisms die, they drop to the ocean floor. Over time, the organic parts decay and the calcium carbonate accumulates to form limestone. Fossil remains of these aquatic animals can often be found in limestone.

Limestone can also be formed chemically when calcium carbonate dissolved in water falls out of solution, and settles to the bottom. It is estimated that there is 200 years of deposition for every inch of limestone created. Limestone layers vary in width, color, and durability due to the many variables in its creation. Sea life, minerals, water depth, and climatic conditions all contribute to the variations found in limestone. Mineral deposits often form in the cracks and pores of limestone. Calcite deposits can be found in the form of geodes and crystals in some layers. Perhaps the most well-known deposits are those from which the hills receive their name. Chert or "flint" is common in many Kansas limestones as nodules or continuous beds. It breaks with a shell-like fracture, and the edges of the broken pieces are sharp. Chert is a sedimentary rock composed of microscopic crystals of quartz (silica, SiO2). It is unknown for sure what the source of silica would have been. However, it has been theorized that it was precipitated from volcanic ash and hardened in cracks and voids of the limestone.Between the layers of limestone are softer silt and clay layers called mudstones or shale. These originated from deposits of suspended clays settling to the bottom and compacting, creating brittle layers of shale. Conditions in the oceans would have been different, perhaps deeper and more turbid waters, to favor shale deposits over limestone.

At the close of the Permian Period many events occurred. Land that is Kansas today experienced many periods of rising and falling sea levels, land movement, and crust shifts. The Rocky Mountains rose creating new weather patterns and erosion that slowly started peeling away the sediments that had been formed so many millions of years ago. Finally, within the last 20,000 years or so, the Flint Hills would have begun to look much like the landscape we have today. The limestone layers with their deposits of chert are more resistant to weathering and remain prominent hilltops, while the softer shales under them erode into the valley and watersheds. This creates the bench and slope, or terraced topography we see on the preserve. As the limestone and the shales erode away the more resistant flint is left behind creating soils that are very rocky.