The City of Cape Town (CoCT) metropolitan municipality seeks to identify and develop alternative water resources for the augmentation of surface water to ensure more robust and sustainable water supply to the CoCT and its inhabitants. A 3-D finite-element numerical model of the Atlantis Aquifer was developed using the commercial code FEFlow 7.1 to support the assessment of the impact of groundwater abstraction from the aquifer which has been identified as one of the target zones to develop sustainable alternative water resources as part of the CoCT water reconciliation strategy. The numerical model acts as a decision support tool to assist in planning and management of the rehabilitation and potential expansion of the groundwater abstraction and managed aquifer recharge scheme. The numerical model is to be applied in determining the impact of additional abstraction as well as assess the maximum sustainable yield from the wellfields without negatively impacting on surface water sources and other groundwater dependent users. The model improves upon previous modelling work and represents the latest and most comprehensive knowledge in terms of three-dimensional aquifer geometry, location and rates of anthropogenic groundwater users, spatial distribution of recharge, hydraulic parameters and location of aquifer boundary conditions. Model parameters have been successfully calibrated under steady-state conditions to provide a realistic representation of long-term groundwater levels across the system (R2=98%). Abstraction scenarios and their impact on groundwater levels were assessed using the calibrated numerical model. Scenarios were simulated of three phases of abstraction (approximately 15, 25 and 40 Ml/d) to determine drawdown around the wellfields, the impact on spring discharge, and the possibility of saline intrusion. Model results show drawdown to be mostly confined to the associated wellfields, with minor drawdown experienced in the vicinity of Silwerstroom. Simulated hydraulic heads indicate that seawater intrusion is unlikely to occur under all scenarios.