Wastewater-based epidemiology (WBE) is a promising approach that has been used to monitoring the exposure to pathogens and understanding the status of disease outbreaks in defined population groups. Viral RNAs of SARS-Cov-2 and influenza A and B were detected and quantified by two commercial kits in three wastewater treatment plants (WWTP) selected in different regions of Canton Ticino (Switzerland). We have monitored the presence of SARS-CoV-2 during two big waves of pandemic, from March 2021 until June 2023, when number of confirmed cases and tests decreased. The presence of influenza A and B viruses was investigated from October 2022 to June 2023. We confirmed the presence of SARS-CoV-2 and influenza A and B in all the WWTP monitored; RNA concentration in wastewater could be correlated with clinical cases confirming that WBE is a powerful tool to monitor diseases dissemination supporting the management of an epidemic.