Analysis of TOC and NO3- contents in the water at four springs in the province of Malaga (southern Spain), sampled under different hydrologic conditions, revealed two different hydrochemical behaviour patterns for these natural tracers of infiltration. TOC content increased during every recharge period, following the rapid arrival of water infiltrating through the soil. On the other hand, NO3- content only rose during the first flood episodes (normally in autumn), and fell during the winter and spring ones. This difference is the consequence of the distinct biogeochemical kinetics of nitrogen with respect to organic carbon, both in the soil and within the aquifer. Unlike the mineralisation undergone by TOC from the surface to the spring, the NO3- ion remains in the aquifer almost unaffected, due to the oxidising conditions prevailing within the karst medium, which impede its denitrification and favour its preservation within the saturated zone. TOC and NO3- have a common origin in the soil and can be used to determine infiltration processes and the hydrogeological functioning of karst aquifers. Their different hydrogeochemical evolution provide information about mineralization and degradation processes of organic matter within karst aquifers, which can be used to validate the vulnerability to contamination in this type of medium.