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. At the same time, δ13CTDIC and nitrate values rise along the subsurface flow. While the carbon isotope evidences a shorter transit time between recharge areas and the top of the saturated zone than the subsequent path toward the permanent base springs, nitrate evolution is affected by pollution sources near discharge areas, so its applicability is questionable. Finally, organic matter (TOC and intrinsic fluorescence) mineralizes (or degrades) up to 90% from the first centimeters of soil to the permanent basal springs. An exponential decreasing trend defines the relationship between TOC and δ13CTDIC caused by organic matter attenuation along the groundwater flow path, while δ13CTDIC increases because of a higher residence time of water in contact with the host rock. These results, together with previous research based on other natural tracers (chemical, isotopes, and dating tools) and dye tracing experiences, permit to link TOC and δ13CTDIC values with a range of transit times, from hours-days to years-decades. Meanwhile, the attenuation of natural intrinsic fluorescence and TOC signal evidence the filter function of the aquifer from the soil to the saturated zone. All these findings highlight the usefulness of natural fluorescence and, particularly, TOC and δ13CTDIC, as tracers of groundwater flow and hydrogeochemical processes within the different compartments of complex karst aquifers.