Serial Biological Concentration (SBC) of salts is an innovative technology to manage salts in agricultural drainage. This approach utilises saline drainage water as a resource to produce marketable crops and, therefore provides a method to manage salts in a viable manner. However, there are associated risks of development of groundwater mound beneath the treatment facility and the consequent threats of groundwater contaminations. The water table in the shallow aquifers often rises to the ground surface following irrigations and rainfall events. In the SBC system, the intensive drainage system manages these events and enables the water table to be lowered rapidly. This paper describes the hydrogeological assessment of an SBC system to quantify the water table mound and the effect on the local groundwater. The deep leakage rates and lateral flows to adjoining lands are determined in order to asses the onsite and regional impacts under typical SBC operation. Modelling results show that the net watertable rise under a 50 ha site, in the first year of the system operation, is about 1.3 meters. However, there is no further water table rise during 25 years of simulated operation, mainly because of the high drainage efficiency of the tile drainage operation in the SBC system. The water table under the SBC site reaches quasi equilibrium with periodic rise and fall around the tile drain depth. The deep leakage beneath the SBC bays is approximately 1mm/day which is around 10% of the saturated groundwater flow above the tile drains. Simulation scenarios of various sizes of the SBC system in its present hydrogeological settings suggest that the lateral extent of groundwater mound does not extend beyond 50 m from the outer edge of its bays. In order to develop SBC systems at other locations, a GIS-based site suitability assessment model is recommended to evaluate the SBC effect under different soil and hydrogeological conditions.