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The present study examined groundwater recharge/discharge mechanisms in the regional Central Sudan Rift Basins (CSRB). Aquifers in CSRB constitute poorly sorted silisiclastics of sand, clay and gravels deposited in closed hydrologic systems of the Cretaceous-Pleistocene fluviolacustrine environments. CSRB are bounded to the north by the highlands of the Central African Shear Zone (CAZS) that represents the surface and groundwater divides. Sporadic recharge in the peripheries of the basins along the CASZ occurs subsequent to decadal and centennial storm events. Inflow from the Nile into the aquifers represents an additional source of recharge. Thus, groundwater resources cannot be labelled fossil nor can they be readily recharged. Closed hydrologic troughs located adjacent to the influent Nile system mark areas of main groundwater discharge characterized by lower hydraulic heads. This study has examined mechanisms that derive the discharge of the groundwater in these closed basins and concluded that only evapotranspirative discharge can provide a plausible explanation. Groundwater abstraction is mainly through deep-rooted trees and effective evaporation. The increase of TDS along the flow indicates local recharge at the peripheries of basins and shows the influence of evaporation and rock/water interaction. The decline in groundwater level along a flow path was calculated using Darcy’s law to estimate average recharge and evapotranspirative discharge, which are equal under natural equilibrium and make the only fluxes in CSRB. Steady-state 2D flow modelling has demonstrated that an average recharge of 4-8 mm yr(-1) and evapotranspirative discharge of 1-22 mm yr(-1) will maintain natural equilibrium in CSRB. Sporadic storms provide recharge in the highlands to preserve the current hydraulic gradient and maintain aquifer dynamics. Simulated recharge from the Nile totals about 17.5 mm yr(-1) and is therefore a significant contributor to the water balance. Copyright (C) 2007 John Wiley & Sons, Ltd.