Conceptual models of the Critical Zone (CZ) have been developed primarily in humid and temperate settings, where subsurface organization is often described as a function of continuous vertical gradients in hydrology, weathering, and biogeochemical development. The extent to which this vertical-gradient framework applies to arid CZs – where water limitation, episodic recharge, and spatially discontinuous resource distributions dominate – remains largely unexplored. Here, we evaluated whether microbial functional organization across an arid CZ follows broad saturated-unsaturated zonation or is instead shaped by localized hydrobiogeochemical heterogeneity. We combined community-level physiological profiles (CLPPs) with analyses of substrate organic matter (OM) quantity and quality (estimated from δ¹³C signatures), substrate texture, and groundwater hydrochemistry from samples collected at multiple depths from eight boreholes spanning the unsaturated-saturated continuum of a groundwater-dependent ecosystem dominated by the facultative phreatophyte <em>Ziziphus lotus</em> (L.) Lam. in an arid Mediterranean setting. Microbial functional responses derived from carbon-source-use patterns were not primarily structured by saturated-unsaturated zonation per se. Instead, OM availability emerged as the dominant driver of both general microbial functional metrics and the utilization of several carbon-source groups, whereas OM quality exerted more selective effects on carbon-source-use patterns, altering the relative importance of different carbon-source groups under increasingly processed OM conditions. Substrate texture modulated these responses, with sandy fractions generally constraining microbial activity, although these effects were partially compensated by higher OM availability. Notably, groundwater-table position, groundwater hydrochemistry, proximity to <em>Z. lotus</em> individuals, and <em>Z. lotus</em> greenness did not emerge as significant drivers. In particular, the absence of relationships with either proximity to <em>Z. lotus</em> or its vegetation greenness indicates that the influence of this phreatophyte may be largely restricted to localized zones rather than extending across the broader subsurface matrix. These findings suggest that microbial functioning in arid CZs may be organized around spatially discontinuous hydrobiogeochemical resource patches and localized habitat heterogeneity rather than around the vertically structured gradients that characterize many humid-climate CZ conceptual models.