Background and Objective: Recent research highlighted the negative impact that climate change has on social and environmental factors that determine human health, such as availability and quality of water resources. In particular Alpine rivers, frequently utilized for different human activities (e.g. drinking and irrigation), are more altered by climatic change showing a general flow rate reduction that can affect water quality. In fact, during the more frequent periods of drought, emissions from anthropogenic sources such as wastewater treatment plant (WWTP) discharges are less diluted determining an increase in the concentrations of pathogenic microorganisms. The aim of this study is to evaluate the wastewater discharge effect on spreading of human pathogens in Alpine rivers in relationship to flow rate reduction. Methods: Samples upstream (U), downstream (D) and at discharge (W) of WWTPs in three Alpine streams were collected monthly for one year. Parameters investigated are: coliforms, enterococci and Escherichia coli quantification using Quanti-TrayTM 2000 (IDEXX Laboratories), Clostridium perfringens spores enumeration using membrane filtration method, presence/absence of Salmonella spp. and verocytotoxin-producing E. coli (VTEC) by PCR. Moreover, also ecological, chemical and hydrological aspects are investigated. Results: Discharge samples (W) showed high contamination by the different indicators, but the effect of WWTP is mainly evidenced in one of the investigated rivers which shows an increase respect to U samples. Salmonella spp. was present in all rivers investigated, but similarly among U and D samples except for one river, indicating other contamination sources. VTEC presence seems to be not related to WWTP discharge. Conclusions: The results obtained so far indicate that WWTP effect is detectable but strongly related to the sampling site underlining the need to monitor the microbiological contamination in river impacted by climatic change reducing human pathogen circulation and the possible indirect effect on human health.