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This article studies the effect of drought and pumping discharge on groundwater supplies and marine intrusion in the Korba aquifer (Cap-Bon peninsula, Tunisia). The Groundwater Modelling System has been used to model the groundwater flow and to simulate the seawater intrusion. The calibration is based on the groundwater levels in the steady state from 1963, and in the transient state from the groundwater levels from 1963 to 2005. The main objective is to quantify the components of the groundwater mass balance and to estimate the hydraulic conductivity distribution. The impact of pumping discharge on the groundwater level evolution has been examined by two pumping scenarios P1 (no. 8420) and P2 (no. 8862) wells. The hydrodynamic modelling shows the increasing drawdowns after 14 years of pumping: 4 m in P1 well and about 5 m in P2 well below sea level. The drawdowns are accompanied by the inverse hydraulic gradient. The numerical model was used to discuss the management of the groundwater resources of Cap-Bon. As the population continues to grow and the demand for groundwater pumping intensifies beyond the 1963 level, it can be expected that the actual extent of seawater intrusion in the future would be more severe than the model prediction. Better strategies for groundwater development and management will be necessary to protect the freshwater aquifers to the marine intrusion. Copyright © 2011 John Wiley & Sons, Ltd.