Traditional aquifer vulnerability techniques primarily rely on spatial property data for a region and are limited by their ability to directly or indirectly assess flow and transport processes occurring from the surface to depth within an aquifer system. The main objective of this study was to investigate groundwater vulnerability in terms of aquifer interconnectivity and flow dynamics. A combination of stable isotopes, groundwater age-dating (radiocarbon), and geomorphic/geogenic spatial analyses was applied to a regional, highly developed coastal aquifer to explain the presence of nitrate at depth. The average δ13C value (−17.3 ± 2‰ VPDB, n = 27) is characteristic of groundwater originating from locally infiltrated precipitation through extensively cultivated soils. The average δ18O and δD values (−4.0 ± 0.1‰ VSMOW, n = 27; δD: −19.3 ± 1‰ VSMOW, n = 27, respectively) are similar to precipitation water derived from maritime sources feeding the region's surface water and groundwater. Stable and radioactive isotopes reveal significant mixing between shallow and deep aquifers due to high velocities, hydraulic connection, and input of local recharge water to depths. Groundwater overdevelopment enhances deeper and faster modern water downward flux, amplifying aquifer vulnerability. Therefore, aquifer vulnerability is a variable, dependent on the type and degree of stress conditions experienced by a groundwater system as well as the geospatial properties at the near surface.