Fecal pollution at beaches can pose a health risk to recreators. Quantitative microbial risk assessment (QMRA) is a tool to evaluate the use of candidate fecal indicators to signify a health risk from enteric pathogens in sewage-impacted waters. We extend the QMRA approach to model mixtures of sewage at different ages using genetic marker concentrations for human-associated crAssphage, Bacteroides spp., and polyomavirus in sewage samples from 49 wastewater facilities across the contiguous United States. Risk-based threshold (RBT) estimates varied across different mixture and sewage age scenarios. Fresh sewage RBT estimates were not always protective when aged sewage was present, and aged sewage RBT estimates often fell below the marker lower limit of quantification. Conservative RBT estimates of 9.3 × 102 and 9.1 × 103 (copies/100 mL) for HF183/BacR287 and CPQ_056, respectively, were predicted when fresh sewage was greater (by volume) than aged at the time of measurement. Conversely, genetic markers may not be effective indicators when aged sewage contributes the majority of pathogens, relative to fresh contamination, but minimal marker levels. Results highlight the utility of QMRA that incorporates pollutant age and mixture scenarios, the potential advantages of a crAssphage fecal indicator, and the potential influence of site-specific factors on estimating RBT values.