- Abstract The Western Mountain Aquifer (Yarkon-Taninim) of Israel is one of the country's major water resources and partially flows through a karst system. During late winter 2013, maintenance actions were performed on a central sewage pipe that caused sewage to leak into the creek located in the study area. Carbamazepine (CBZ) was used as an indicator for the presence of sewage in the groundwater. The research goal was to develop a mathematical model for quantifying flow and contaminant transport processes in the karst/fractured-porous unsaturated zone and groundwater system. The model was used to simulate CBZ transport during and after an observed sewage leakage event. A quasi-3D dual permeability numerical model represents the 'vadose zone – aquifer' system, by a series of 1D vertical flow and transport equations solved in a variably-saturated zone and by 3D-saturated flow and transport equation in groundwater. The results of simulation showed that after the leakage stopped, significant amounts of CBZ were retained in the porous matrix of the unsaturated zone below the creek. Water redistribution and slow recharge during the dry summer season contributed to a continuous supply of CBZ to the groundwater in the vicinity of the creek and hundreds of meters downstream.