Groundwater Flow Modelling of a Large-Scale Thick Vadose Zone Including Two Perched Aquifers, the Jerusalem Mountains

In mountainous karst terrains, understanding flow dynamics within thick, stratified, and faulted vadose zones remains a major hydrological challenge. This study examines a dual-perched aquifer system on a folded limestone ridge near Jerusalem, Israel, where groundwater accumulates above low-permeability layers and transfers vertically along faults. Using a fully three-dimensional FEFLOW model, we simulate the coupled processes of infiltration, perching, and leakage, and identify the spatial fragmentation of perched reservoirs into hydraulically discrete spring catchments. Despite sparse borehole data, the model, calibrated with high-resolution spring hydrographs and daily precipitation, effectively captures key flow behaviours and quantifies storage–release dynamics across unsaturated strata. The structural controls and flow mechanisms discovered in this system, especially fault-mediated vertical coupling between perched and regional groundwater and the compartmentalisation of saturated zones, are likely common in other fractured karst uplands. Accordingly, the modelling approach developed here offers a transferable method for mapping recharge areas, managing distributed spring systems, and evaluating vulnerability to contamination. These insights are particularly relevant for hydrogeological assessments and groundwater management in densely populated, data-scarce mountainous regions increasingly affected by hydroclimatic variability.