Water availability controls the functioning of dryland ecosystems, driving a patchy vegetation distribution, unequal nutrient availability, soil respiration in pulses, and limited productivity. Groundwater-dependent ecosystems (GDEs) are acknowledged to be decoupled from precipitation, since their vegetation relies on groundwater sources. Despite their relevance to enhance productivity in drylands, our understanding of how different components of GDEs interconnect (i.e., soil, vegetation, water) remains limited. We studied the GDE dominated by the deep-rooted phreatophyte Ziziphus lotus, a winter-deciduous shrub adapted to arid conditions along the Mediterranean basin. We aimed to disentangle whether the groundwater connection established by Z. lotus will foster soil biological activity and therefore soil fertility in drylands. We assessed (1) soil and vegetation dynamics over seasons (soil CO2 efflux and plant activity), (2) the effect of the patchy distribution on soil quality (properties and nutrient availability), and soil biological activity (microbial biomass and mineralization rates) as essential elements of biogeochemical cycles, and (3) the implications for preserving GDEs and their biogeochemical processes under climate change effects. We found that soil and vegetation dynamics respond to water availability. Whereas soil biological activity promptly responded to precipitation events, vegetation functioning relies on less superficial water and responded on different time scales. Soil quality was higher under the vegetation patches, as was soil biological activity. Our findings highlight the importance of groundwater connections and phreatophytic vegetation to increase litter inputs and organic matter into the soils, which in turn enhances soil quality and decomposition processes in drylands. However, biogeochemical processes are jeopardized in GDEs by climate change effects and land degradation due to the dependence of soil activity on: (1) precipitation for activation, and (2) phreatophytic vegetation for substrate accumulation. Therefore, desertification might modify biogeochemical cycles by disrupting key ecosystem processes such as soil microbial activity, organic matter mineralization, and plant productivity.