In 2022, several cases of acute hepatitis of unknown etiology (AHUE) have been associated with Adeno-associated virus 2 (AAV-2) and the common childhood virus Adenovirus 41 (AdV-41). This outbreak has resulted in serious complications in patients which included 5 % of individuals requiring a liver transplant and 22 deaths. Before these AHUE cases, no previous information had been reported regarding the co-infections and co-occurrence of these two viruses in the human population. The present study utilized WBE tools to investigate the prevalence of AAV-2 and AdV-F (AdV-41 and AdV-40) in wastewater from two different waste-water treatment plants (WWTP) serving the city of Bloomington in Southern Indiana, USA. The concentrations of AAV-2 and AdV-F were quantified using digital PCR in weekly wastewater samples taken over the duration of 18 months. High levels of both viruses were observed in most of the samples where co-detection and correlation in the concentrations for AAV-2 and AdV-F were found to be significant (p < 0.01) throughout duration of the study. In addition, significant seasonal changes were observed in the viral concentrations of both viruses (P < 0.01), but these seasonal variations were different between WWTPs (p < 0.01). However, these seasonal variations in viral concentrations were similar for both viruses. The sequences of AdV-F and AAV were obtained from the wastewater samples and confirmed the detection of AAV-2, AdV-41, and AdV-40 in the samples analyzed. Even though our study was done after the 2022 outbreak of AHUE, our results demonstrated the persistence of infections with both viruses in the population. It also highlights the ongoing spread of both viruses in the population and the importance of WBE in surveillance of these viruses.