Although the fractured aquifer of the Salento supplies over 80% of the drinking water requirements of the local population, its exposure to pollution has recently increased. In recent years, owing to the arid climate and droughts, the spreading of wastewater on soil for irrigation has become much more frequent. Consequently, hazardous and pathogenic microorganisms released with wastewater have been transported into the subsoil and have contaminated groundwater. An elaboration of epidemiological data has shown that the local population has the highest exposure to endemic gastroenteritis in Italy. In order to reduce human exposure to unsafe groundwater, the setback distance for drinking wells necessary to achieve the 'natural disinfection' criteria, has been determined experimentally at the Nardò aquifer (Salento region), supported by groundwater monitoring results and a mathematical transport model able to determine the apparent pathogenic microorganism pathways in fractures. The results also provided valuable inactivation constants of cultural indicators (coliforms, enterococci, Clostridium spores and somatic coliphages) and viruses in the wastewater that have been injected into the fractured aquifer since 1991. Furthermore, the efficacy of chlorine to remove viral indicators from water in a well 500 m from wastewater injection was tested. Hypochlorination reduces somatic coliphages and Clostridium spores in groundwaters but did not achieve complete inactivation in all tests. Complete disinfection of groundwater samples was possible only when there was an initial Clostridium spores count of ≤ 10CFU 100 ml-1. © IWA Publishing 2007.