A numerical model for the NCMA aquifer complex is presented. The objective of the study is to develop a numerical groundwater model for the NCMA aquifer system to enhance the understanding of subsurface groundwater flow. Infiltration, streamflow, pumping, and return flows are implemented to characterize the aquifer complex over time. The numerical model is calibrated to municipal and monitoring well data, average monthly water balances, and hydraulic contours. Transient aquifer inflows and outflows are assessed in the results of the study and are compared to balance terms from previous studies. The 2007 Todd Engineers Study subsurface inflows and outflows generate well hydrographs that have greater heads than observed data. Calibration to well hydrographs generated increased subsurface outflow values and decreased subsurface inflow values. It is possible that approximately 250 AFY is leaving aquifer storage.