During the COVID-19 pandemic, wastewater-based epidemiology (WBE) became an effective method for tracking the spread of SARS-CoV-2 across the world. This inspired the scientific community to investigate which other microbes could be measured in wastewater. The present study compares Influenza A and SARS-CoV-2 viral counts between November 2022 and March 2023 in wastewater from Meridian, Idaho. Influenza A was reliably detected in wastewater during fall and winter months and its viral counts have a weak positive correlation with SARS-CoV-2 counts. The correlation from multiplex (multiple target) analyses opens an area of research to establish the factors that influence viral prevalence and detection in wastewater.