Wetlands and the species that utilize can act as critical hot spots for the spread of various pathogens. High Pathology Avian Influenza (HPAI) is a significant disease threat for both domestic and wild avian species, especially waterfowl. Despite this pathogen affecting both wild and domestic species most of the tracking and diagnostic efforts focus on domestic species while wild birds, especially waterfowl are largely overlooked. Waterfowl utilize a wide range of environments ranging from large undisturbed wetlands to heavily altered and man-made ponds. Current methodology for confirming and tracking HPAI in wild birds relies on data from mass die-off events or hunter harvested kills. However, eDNA and genomics technology are advancing to the point of affordability and reliability to allow researchers to use these techniques to track and predict outbreaks. In this study we utilized genomics techniques to sample water from six locations along the South Carolina coastline spanning ~50 miles of coast and multiple different habitat types. Using a peristaltic pump and 0.2-micron eDNA filters we collected water samples monthly throughout the migratory and active hunting season (November 2025 – April 2026) for common and commercially important waterfowl. Using viral RNA extraction kits, we extracted and amplified viral fragments from our samples. Samples positive for the presence of RNA were sent to the South Carolina State Diagnostic Laboratory for confirmation of HPAI via qPCR. We predict that our sample detection will vary with both with seasonality, November – January will have higher detections compared to February – April, and disturbance, heavily disturbed and altered habitats showing higher or more frequent detections of HPAI and other pathogens. This study will be able to highlight key times to sample these critical habitats allowing for more active management of these wetlands to stem and slow the spread of these pathogens.