Prospective influenza A (IAV) RNA monitoring at 190 wastewater treatment plants across the US identified increases in IAV RNA concentrations at 59 plants in spring 2024, after the typical seasonal influenza period, coincident with the identification of highly pathogenic avian influenza (subtype H5N1) circulating in dairy cattle in the US. We developed and validated a hydrolysis probe RT-PCR assay for quantification of the H5 hemagglutinin gene. We applied it retrospectively to samples from three plants where springtime increases were identified. The H5 marker was detected at all three plants coinciding with the increases. Plants were located in a state with confirmed outbreaks of highly pathogenic avian influenza, H5N1 clade 2.3.4.4b, in dairy cattle. Concentrations of the H5 gene approached overall influenza A virus gene concentrations, suggesting a large fraction of IAV inputs were H5 subtypes. At two of the wastewater plants, industrial discharges containing animal waste, including milk byproducts, were permitted to discharge into sewers. Our findings demonstrate wastewater monitoring can detect animal-associated influenza contributions, and highlight the need to consider industrial and agricultural inputs into wastewater. This work illustrates wastewater monitoring’s value for comprehensive influenza surveillance for diseases with zoonotic potential across human and animal populations.