This study demonstrates the significant influences of the geological structure (especially folding and lithology) and the karst system on groundwater flow regime. Folds divert groundwater flow from the general hydraulic gradient; marly layers sustain several perched sub-aquifers above the regional aquifer; and karstification increases the hydraulic conductivity by several orders of magnitude. These phenomena are quantitatively demonstrated within the Yarqon-Taninim (YT) basin, Israel, which is a complex groundwater system, combining several (extremely) opposite characteristics: humid and arid recharge zones, phreatic and confined parts, shallow and deep sub-aquifers, stratified and relatively-homogeneous sub-basins, saline and fresh water bodies, as well as stagnant and fast-flowing groundwater regions. We have introduced a 3D geological-based grid for the basin (for the first time). It was implemented into a numerical code (FEFLOW), which was used thereafter to analyze quantitatively the flow regime, the groundwater mass balance, and the aquifer hydraulic properties. We present up to date conceptual understanding and numerical modeling of the YT flow field, especially at its mountainous parts. Based on the calibration procedure and the sensitivity analyses, we obtained the best-fitted hydraulic conductivity values for the aquifer mesh. The general phenomenon observed is that as groundwater flow quantity increases, the hydraulic conductivity also increases. We interpret this result by the karstification mechanism (including paleo-karst). Thus, where groundwater flow-lines converge and where groundwater discharge amount increases, the karstification process intensifies and permeability increases. Consequently, at the mountainous region, along the syncline axes, where groundwater flow-lines converge, higher conductivities are found. Modeling results also exhibit that at the lowland confined area, the geological structure does not play a major role in directing groundwater flow. Rather, the flow field is controlled by the well-developed karst system and the relatively homogenous carbonate section. It is hypothesizes that the extensive karstification took place at the Messinian Salinity Crises, ∼5.5 Ma, during which groundwater heads as well as sea level were lowered by several 100 m.
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