Basins of this type are sites where sediments accumulate over long periods of time (millions of years). These sediments were mostly deposited in shallow to deep seawater in an environment similar to that of a modern sea or gulf. As the deposits of sediments began to build up, the underlying crust was depressed by the additional weight. For about 330 million years, thousands of feet (vertical thickness) of sediments continued to be deposited in mostly marine conditions in the basin, which had evolved into an elongated trough. As this burying process continued, older and deeper sediments were compacted and converted into rocks (e.g., sandstone, shale, and limestone). At the beginning of the Pennsylvanian Period (320 m.y.), significant terrestrial (land) sediments, intermixed with marine deposits, began to accumulate in the Basin. Some of the terrestrial deposits later formed coalbeds. Near the end of the Pennsylvanian Period and into the Permian Period, the southern end of the Basin was deformed and uplifted, forming the present-day spoon-shaped Basin, as well as the structures that now exist as the Shawnee Hills.
During the age of the reptiles and dinosaurs (the Mesozoic Era), most of the Illinois Basin was probably a tropical and terrestrial environment. There are, however, no rocks of the Triassic (251-202 m.y.) and Jurassic (202-145 m.y.) periods in the Basin. This means that during these two periods, either rocks were primarily being eroded, or if strata were deposited, they were subsequently eroded. Rocks of the third period of the Mesozoic Era, the Cretaceous (145-65 m.y.), are present in small areas of western and southern Illinois. This suggests that during the Cretaceous Period, both erosion and deposition of sediments took place within the Basin. This trend continued during the Tertiary Period as these deposits occur in the extreme southern part of the Basin and in scattered outcrops, mostly in the western part of the Basin. To summarize most of the last 250 million years, the Illinois Basin probably has been subjected to more erosion of rocks rather than the deposition of rocks. It has been estimated that a thickness of about 5,000 feet of strata have been eroded from the central part of the Basin during this very long time period.
The last significant period of deposition occurred during the Pleistocene Epoch (also known as the Ice Ages), which began about 2.5 million years ago. During this time, the climate repeatedly fluctuated between cold glacial episodes (when glaciers advanced from Canada to the south) and warm interglacial episodes (when glaciers melted, or "retreated" back to the north). During the largest glacial advance (the Illinoian), more than 90% of the state of Illinois was covered in ice. The last glacier (the Wisconsian) retreated from the Basin about 13,000 years ago. Glaciers both eroded and deposited sediment, but most of the sediments are deposited at the terminal areas of the glaciers, which is where the Illinois Basin was situated. As a consequence, much of the Illinois Basin is covered by a fairly thick succession of glacial sediments (also known as drift).