Contaminants of emerging concern (CECs), such as pharmaceuticals, personal care products, and industrial chemicals, are increasingly detected as complex mixtures in freshwater environments, primarily due to wastewater discharge and urban activities. These contaminants may affect bacterial persistence and physiological states, potentially altering the abundance and detectability of bacteria in aquatic ecosystems. As fecal indicator bacteria (FIB) are essential for assessing microbial water quality, it is critical to determine whether their indicator performance is compromised under CEC exposure. This study evaluates the impact of environmentally relevant CEC mixtures on the reliability of Escherichia coli and Enterococcus faecalis as indicators in freshwater. The CEC mixtures were formulated based on the composition and concentrations observed in urban streams in Busan, Republic of Korea, to reflect realistic exposure scenarios. Following exposure, we determined culturable, viable, and total bacterial abundances using plate counting, quantitative PCR (qPCR), and propidium monoazide-qPCR (PMA-qPCR), respectively. By integrating these complementary approaches, this study aims to assess whether CEC exposure influences the persistence of FIB and, consequently, their suitability for microbial water-quality monitoring in chemically altered freshwater environments.