Protection of karstic groundwater quality can be successful only if it is based on reliable reconstructions of conceptual models of the karstic aquifers, which are normally of high complexity: this requires the integration of classical hydrogeological information with that obtainable by using natural tracers, according to multi-tracing methods. The definition of the conceptual model includes elements as the identification of recharge areas, their connection with discharge areas, the sequence of physical – chemical processes acting into the aquifer and the transport mechanisms. With reference to the identification of recharge areas, two casestudies are illustrated. The first deals with a continental karstic aquifer (Monti Simbruini, Central Italy) discharging through springs used for drinking purposes: it has been studied by using the stable deuterium and oxygen-18 isotopes according to the “mass-center” method coupled with the “inverse hydrogeological budget” method. The second regards a platform karstic aquifer (Murgia, Southern Italy), discharging through coastal brackish springs, which is exploited by wells for both drinking and agricultural purposes: for recognizing some elements of the conceptual model a multi-tracing approach has been adopted, which uses the crossverification of information coming from the interpretation of isotopic, chemical and physical tracers. Moreover, with the aim of outlining the factors that control the pollutant transport in karstic aquifers, two case-studies related to Murgia aquifer illustrate a first method for defining the hazard due to direct injection of effluents from treatment plants and a second approach for defining, through monitoring data, the transport mechanisms of pollutant released at land surface.