To reduce the amount of testing and cost necessary to generate representative wastewater surveillance of influenza A virus (IAV) data for small public health units (PHU) in large geographic areas with small and dispersed municipalities, we compared the wastewater (WW) viral activity level (VAL) metric, developed by the United States Centers of Disease Control and Prevention (CDC) to the raw data and viral load to better interpret the relationship between WW signal and weekly number of positive clinical cases. We assessed two small PHUs in Ontario, Canada, and with just 21–27% coverage of the PHUs’ populations, WW surveillance for IAV viral RNA, viral load, and raw WW signals was able to obtain strong positive Kendall’s τ correlations with PHUs’ IAV clinical cases, showing (0.59–0.85) and (0.77–0.93), respectively. The VAL also helped identify towns with higher-than-expected levels of IAV. Measurement of other WW parameters and assessment of sewer infrastructure provided explanations for the differences observed between each WW treatment plant and its respective PHU. Overall, we demonstrated that minimal sampling within a small PHU, supported by careful consideration of sewer infrastructure and the location of WW treatment plants, can provide an accurate, efficient, and cost-effective approach for IAV surveillance.