This dissertation investigates the fate of different sewage associated viruses and bacteria in environmental waters so to inform best practices for water quality management. The four main objectives addressed in this dissertation were to (1) understand the persistence of fecal indicator bacteria (FIB), viral indicators and pathogens in model freshwater systems, (2) characterize the particle associations of promising molecular fecal pollution indicators, (3) determine the transport characteristics of bacterial and viral indicators in flowing waters, and (4) determine the persistence of infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater and water. The results of these investigations will help develop promising viral fecal indicators for water quality monitoring purposes where they can improve upon the traditionally used fecal indicator bacteria (FIB) and other proposed bacterial indicators. Additionally, this research will also address the concerns around the handling of wastewater by examining the persistence of emerging pathogen, SARS-CoV-2, in water and wastewater. Ultimately, the results from this research will help with risk assessments protecting the general public, maintenance personnel and scientists around the world in contact with wastewater.