The factors governing the groundwater flow in an aquifer can be investigated extensively if comparisons can be made to similar aquifers with slightly different geologic materials. For this study two different aquifers were modeled in similar areas of central Illinois, along the Illinois River in North Pekin and Mississippi Rivers in Pike County. These areas were modeled to investigate the flow dynamics of each and to delineate Wellhead Protection Areas for the Illinois EPA’s Wellhead Protection Area Program. Each area consists of different geologic materials. The North Pekin area is a valley fill aquifer consisting of clean medium-grained sands, the Pike county area is an glacial outwash aquifer made of poorly sorted sands and gravels. However, these materials are close enough in their hydraulic characteristics that comparisons can be made in their flow dynamics. Differences in hydraulic conductivity had the biggest influence on the sensitivity analysis for the North Pekin model, but recharge was the most sensitive to changes in the Pike County model. Changes in bedrock topography and groundwater extraction from the aquifers had little effect on the numerical simulations. The shape of the WHPAs differed in each area, but were both suprisingly small, confirming the influence of the thickness of the aquifers and its hydraulic conductivity.