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The Grombalia aquifer constitutes a complex aquifer system formed by shallow, unconfined, semi-deep, and deep aquifers at different exploitation levels. In this study, we focused on the upper aquifer, the Wadi El Bey coastal aquifer. To assess natural aquifer recharge, we used a novel physiography-based method that uses soil texture-dependent potential infiltration coefficients and monthly rainfall data. The developed transient flow model was then applied to compute the temporal variation in the groundwater level in 34 observation wells from 1973 to 2020, taking into account the time series of spatially variable groundwater recharge, artificial groundwater recharge from 5 surface infiltration basins, pumping rates on 740 wells, and internal prescribed head cells to mimic water exchange between the wadis and aquifer. The quantified deviations in the computed hydraulic heads from measured water levels are acceptable because the database used to construct a scientifically sound and reliable groundwater model was limited. Further work is required to collect field data to quantitatively assess the local inflow and outflow rates between surface water and groundwater. The simulation of 12 climate scenarios highlighted a bi-structured north—south behaviour in the hydraulic heads: an increase in the north and a depletion in the south. A further increase in the pumping rate would, thus, be severe for the southern part of the Wadi El Bey aquifer. [ABSTRACT FROM AUTHOR]