Climate change and anthropogenic development considerably influence groundwater resource distribution and conditions. Catchment basin groundwater recharge—discharge computation reliability is needed for effective groundwater management policy formulation and implementation and also for resolving environmental challenges in such a watershed. This paper compares groundwater recharge patterns between urbanized and nearly natural small catchment basins of Israel’s Western Mountain Aquifer (WMA). The correlation between precipitation volumes and surface runoff shows that surface runoff volume constitutes 3–4% of the precipitation volume in the Natuf catchment and 1–2% in the Te’enim catchment. These assessments reflect the differences in the land use, outcrop lithology, topography and hydrodynamic properties of the WMA within the model basins. A groundwater recharge assessment based on water balance and water table fluctuation methods was performed for the mountainous karstic Te’enim and Natuf catchment basins for all the available data from 2000 to 2020. The water balance method provided reliable estimates. The groundwater recharge assessment considered land use classification and climate changes during this period. The average multiannual groundwater recharge values for the 2000–2021 period varied from 17.6 × 106–24.8 × 106 m3 to 24.5–29.2 × 106 m3 for the Te’enim and Natuf catchment basins, respectively. For the relatively dry period of the 2013/2014–2017/2018 hydrological years when detailed measurements of the surface runoff were available, the corresponding groundwater recharge volumes were 17.6 × 106 m3 and 24.5 × 106 m3. The corresponding local groundwater recharge coefficients constitute 0.46–0.57 for the mostly agricultural Te’enim basin and 0.29–0.32 for the urbanized Natuf basin. A significant difference in the groundwater recharge coefficients between the studied catchments is caused mostly by the differences in land use. It is suggested that applying such a groundwater recharge estimation for small hydrological sub-basins can improve one’s understanding of the groundwater recharge distribution within a major basin, enabling the application of an accurate regional hydrogeological model that may be extrapolated to other similar regions.
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