Understanding infiltration pathways throughout the different compartments of karst systems (soil-epikarst-unsaturated zone-saturated zone) is vital to assess recharge processes, vulnerability to pollution, and the general hydrogeological functioning of these kind of aquifers. To gain deeper insight into the soil-water-rock hydrogeochemical processes occurring throughout the vertically hierarchized compartments of the aquifer and to evaluate the applicability of different soil natural parameters as groundwater flow tracers, the present work analyzes the spatial and temporal evolution of total organic carbon -TOC-, intrinsic fluorescence related to organic matter, nitrates, δ13CTDIC, and the values of stable isotopes of δ2H and δ18O from water molecules and at different sampling points in a geologically complex karst aquifer in south Spain (Jarastepar carbonate massif). Over two years, rain and soil water (30 and 60 cm deep) samples were collected simultaneously at an experimental plot along with groundwater from the top of the saturated zone and a base-level spring. Results show that the variation in the concentration of natural soil tracers and the signal of water stable isotopes (δ2H and δ18O) smooth throughout the different compartments of the aquifer, with rapid variations in the unsaturated zone after recharge events and delayed effects in the saturated zone.