The Cambrian-Vendian aquifer system is the most exploited groundwater resource in northern Estonia. As a result, the extensive use of groundwater has caused changes in the direction and velocity of groundwater flow in the Tallinn area. A groundwater flow and transport model of the Kopli Peninsula was built to investigate the upconing of saline water from an underlying layer, due to overexploitation of groundwater. A transient flow model was run in different flow regimes, using the pumping and water head data from the years 1946-2007. The vertical conductivity of crystalline rocks and the lower portion of Cambrian-Vendian rocks was found to be of the greatest importance for the range and shape of upconing phenomena. The results of the current study show that the range of the upconing process is dependent on the depth of the well screen interval. Therefore the results of many previous studies can be biased by the leaking of water from the underlying crystalline basement. The results also suggest that leakage from an underlying layer can be minimized by changing the screen depth of production wells.