Three dimensional numerical flow modelling has become one of the best tools to optimise and management wellfields across the world. This paper presents a case study of simulating an existing wellfield in an alluvial aquifer directly recharged by a major perennial river with fluctuating head stages. The wellfield was originally commissioned in 2010 to provide a supply of water to a nearby Mine. Ten large diameter boreholes capable of abstracting ±2 000 m3 /hour were initially installed in the wellfield. The numerical groundwater flow model was used to evaluate if an additional 500 m3 /hour could be sustainably abstract from the alluvial aquifer system. A probabilistic river flow assessment and surface water balance model was used to quantify low and average flow volumes for the river and used to determine water availability in the alluvial aquifer over time. Output generated indicated that the wellfield demand only exceeded the lowest 2% (98th percentile) of measured monthly river flow over a 59 year period, thereby proving sufficient water availability. Conceptual characterisation of the alluvial aquifer was based on previous feasibility studies and monitoring data from the existing hydrogeological system. Aquifer parameters was translated into the model discretisation grid based on the conceptual site model while the MODFLOW River package was used to represent the river. Actual river stage data was used in the calibration process in addition to water levels of monitoring boreholes and pump tests results. The input of fluctuating river water levels proved essential in obtaining a low model error (RMSE of 0.3). Scenario modelling was used to assess the assurance of supply of the alluvial aquifer for average and drought conditions with a high confidence and provided input into further engineering designs. Wellfield performance and cumulative drawdown were also assessed for the scenario with the projected additional yield demand. Scenario modelling was furthermore used to optimise the placement of new boreholes in the available wellfield concession area.