Before the first geological surveys of the state of Kansas in 1864 and 1865, Euro-American geologists knew relatively little about geology in the western half of the state. At that time, Kansas was home to Indigenous groups such as the Kansa, some of whom had important connections to local geological features. Inhabitants of the Flint Hills, for example, had been using the region’s plentiful chert deposits to create stone tools for thousands of years before contact with Europeans. Other features held religious importance: a 28-ton red Sioux quartzite boulder (which was pushed into Kansas by glaciers during the last Ice Age) marked a place of worship for the local Kansa people before the U.S. government forced them out of the area in the 19th century.

In 1864, the Kansas legislature ordered the first geological survey of the state, to be followed by a second survey in 1865. The first survey was conducted by Benjamin Franklin Mudge and a team of 5 scientists—only one of whom was a geologist. Mudge and his successor George Swallow formally documented Kansas’s geological features for a Euro-American audience for the first time and remarked upon many of the same features that Indigenous peoples had made use of before them.

Colonization continued westward in the decades after the Civil War, and by the turn of the century most Indigenous peoples had been pushed out of the region to make room for more white settlers. The state legislature did not fund a permanent geological survey during this same time period, so geology experienced a lull, though geologists continued studying the state's features without public monies.

The Kansas State Geological Survey was established in 1889 at the University of Kansas, informally led by the geologist Erasmus Haworth. Haworth organized the Survey’s first fieldwork and published much of his early research in the University Quarterly. He focused on geological research, while his colleague Samuel Williston began the Survey’s paleontological work. Much of the Survey’s early work also focused on petroleum and coal deposits in Kansas. Students did most of the fieldwork under Haworth's or Williston's supervision.

In 1895, the University of Kansas officially recognized the Survey and placed it under KU administrative leadership. Haworth’s tenure lasted another 20 years before he left the Survey in 1915.

Haworth’s successor, Raymond Cecil Moore, led the Survey for 57 years. In 1931, he published a paper pioneering the concept of cyclic sedimentation, and in 1948 he published the first volumes of the groundbreaking Treatise on Invertebrate Paleontology. Work on the Treatise continues into the present, with new volumes still being written.

Under Moore, the Survey grew both in size and in scientific importance. In 1938 the Survey and the Kansas Geological Society created the first Well Sample Library, located in Wichita, KS. By 1940, the Survey had 20 full-time employees and worked in a supportive role on various projects with the United States Geological Survey (USGS). Moore repeatedly tried to separate the Kansas Geological Survey from KU.

World War II created an increased demand for coal and oil, and the Survey’s work shifted focus to help the war effort. After World War II ended, demand for oil continued to increase throughout the 1950s, and fossil fuel extraction became one of the Survey’s most important areas of study.

In the 1960s and 1970s, as computational tools became more available, the Survey continued to increase the scope of its research. New work in fields such as environmental geology and geophysics became more common, as well as mathematical geology.

The Survey was thrust into the limelight in the late 1960s when Kansas Governor Robert Docking commissioned them to examine a proposed nuclear waste disposal site in an abandoned salt mine in Kansas. In part due to concerns expressed by the Survey’s research team, the project was cancelled.

In the 1970s, the Survey began its work on groundwater, specifically the depletion of the Ogalalla Aquifer. This work continues into the present day, as water from the Aquifer continues to be pumped out faster than it is replenished.

Today, the Kansas Geological Survey has more than 100 employees across locations in Lawrence and Wichita. Scientists at the Survey complete research on subjects such as seismology, geohydrology, and carbon sequestration.