Wastewater treatment plants (WWTP) are natural aggregators of pathogenic organisms due to the waste they treat. This study examined the fate of two bacterial indicators, fecal coliforms (FC) and Salmonella, and one viral indicator, Male-specific coliphages (MSCs), throughout an advanced WWTP. Samples were collected from various points in the WWTP from August 2011 to October 2012. Results show both bacteria and viruses preferentially partition into solids and significant reductions in both bacteria and viruses occur prior to final disposal. The total log removals of FC, Salmonella, and MSCs were 4.51, 5.17, and 6.19, respectively for the solids; and the total log removal of FC, Salmonella, and MSCs in liquids was 4.47, 5.16, and 3.62, respectively. This study provides the first holistic survey of bacteria and virus indicator fate in a WWTP. Furthermore, results herein demonstrate that current biosolids liming regulations may underestimate the level of viruses in Class B biosolids.