The Great Bend Prairie freshwater alluvial aquifer in south-central Kansas overlies a bedrock brine aquifer of Permian age. The continuous extraction of freshwater mainly for irrigation in this area has accelerated the upward movement of the saltwater, resulting in the deterioration of water quality. Predicting saltwater upconing is critical for maintaining a long-term supply of water of good quality to the Groundwater Management District No. 5. This paper uses a numerical model to predict the effect of saltwater upconing on the salinity of pumped water. A sensitivity analysis was conducted for estimating the effects of uncertainties in model parameters on the numerical results. The most important factors affecting the salinity of discharged water are found to be the location and nature of clay layers in the aquifer, the pumping rate, the location of the well screen, and the hydraulic conductivities of the medium. The effect of uncertainties in aquifer porosity and dispersivity on salinity is appreciable but not substantial, whereas that of recharge from precipitation in the study area is relatively insignificant. In addition, a numerical model based on the field conditions observed at the Siefkes site was constructed and calibrated to reproduce and project the variation of measured water levels and discharged groundwater concentration. Finally, a number of practical management recommendations based on this study are presented.