In order to verify the microbial quality of the influents and effluents of one STP from southern Brazil, an eight-month survey was conducted to examine the presence of total and fecal coliforms and of adenovirus (HAdV), enterovirus (EV), genogroup A rotaviruses (GARV) and Torque teno virus (TTV), in treated effluent samples from São João/Navegantes STP, Porto Alegre (Brazil). A total of 16 samples were collected, eight of influent (raw sewage, prior to treatment), and the other eight of the effluent (post-treatment sewage). Total and fecal coliform levels ranging from 3.6 × 10(4) to 4.4 × 10(7) MPN/100 mL and 2.9 × 10(3) to 1.7 × 10(7) MPN/100 mL, were detected in all samples. In raw sewage, HAdV (25%) and GARV (28.6%) viral genomes were detected. The analysis of effluent samples revealed the presence of HAdV (50%), EV (37.5%), and TTV (12.5%) genomic fragments. All samples, regardless of the month analysed, presented detection of a least one virus genus, except for in April. Higher virus detection rates were observed in treated sewage samples (62.5%), and in 80% of them (effluent positive samples) HAdV was detected. Results showed that improvements in sewage monitoring and treatment processes are necessary to reduce the viral and bacterial load on the environment in southern Brazil. To the knowledge of the authors, this is the first study showing the monitoring of viral genomes in influent and effluent samples from a STP located in Porto Alegre (Rio Grande do Sul, Brazil), southern Brazil.