Groundwater flow and water quality in karst aquifers are commonly inferred from point-scale observations, such as spring chemistry and tracer tests conducted near discharge zones. While these approaches are valuable, their interpretation is often ambiguous in structurally complex and compartmentalized aquifer systems, where faults, lithological heterogeneity, and thick vadose zones exert strong controls on flow paths. In this study, we demonstrate how the integration of long-term hydrochemical surveys, tracer experiments, and a calibrated hydrogeological model improves the understanding of groundwater compartmentalization and flow dynamics in a faulted karst aquifer system in the Jerusalem Mountains. A regional hydrochemical dataset collected over multiple years was analyzed using principal component analysis (PCA), revealing distinct spatial clusters governed by lithological and anthropogenic controls. Variations in magnesium concentrations reflect differences in dolomitic section thickness, whereas nitrate and chloride concentrations indicate the influence of urban and rural wastewater sources and their temporal evolution following the upgrading of regional sewage infrastructure. These results provide a broad spatial framework for identifying hydrogeologically distinct zones within the mountain aquifer system. At the local scale, tracer experiments revealed both rapid karstic flow velocities along preferential pathways and the apparent absence of hydraulic connection from nearby injection points. Interpretation of these contrasting responses using a previously published, calibrated groundwater flow model demonstrates that fault-controlled flow diversion explains the observed tracer behavior and supports the subdivision of the aquifer into structurally controlled sub-compartments feeding individual springs. Our findings highlight the limitations of relying on isolated chemical analyses or tracer tests for recharge delineation and spring protection. Instead, we show that independent field observations provide critical validation for physically based hydrogeological models, which offer a robust and spatially consistent framework for groundwater management, protection zoning, and land-use planning in complex karst environments.