The Upper Cottonwood Watershed and Lower Cottonwood Watershed are located primarily in Marion County and Chase County, respectively, in Eastern Kansas. The Cottonwood Watershed headwaters arise the Flint Hills of Eastern Kansas.  The Flint Hills are Permian rocks, which are light-gray to cream-colored limestone, chert, and dark color shale.  Chert forms the escarpments in the Flint Hills.  The Permian rocks are overlain by unconsolidated sediments especially in the riverbeds and streams.  The Cottonwood River in Kansas flows in a southeasterly to easterly direction and empties in the Neosho River in Lyon County.

Eighteen (18) EPA stations, which cover the entire watershed evenly, are used for this research. The Flint Hills surface water is characterized by a high total dissolved solids and total hardness concentrations. The ions Ca²⁺ and HCO₃^- predominate due to the weathering of limestone by precipitation containing CO₂. Other ions include magnesium, sodium, chloride, and sulfate. High levels of silica, magnate, and iron can also be found in the surface water samples. Piper diagram demonstrates that the hydrochemical facies are of calcium type and bicarbonate type. Stiff diagram tells us that the Cottonwood Watershed has a greater concentration of all ionic species than average rivers. The two types of diagrams reveal that the dominant cation is Ca²⁺ and the dominant anion is HCO₃^-.

The local chemical weathering through the interaction between the local specific rocks (limestone and chert) and surface water dominantly controls the chemical characteristics of surface water.