Emergent and submersed aquatic vegetation provide hotspots for food resources and their distribution, which are essential elements of large, oligotrophic riverine systems. A complete understanding of riverine system dynamics must include submersed aquatic vegetation (SAV) diversity and distribution to assess faunal habitat, water flow, sediment stabilization, water quality, and SAV contribution to biogeochemical cycling for food resources. However, spatial data are typically compiled from riverine transects and/or point-intercept surveys, which can be time-consuming, logistically challenging, and costly, particularly for large river systems. The Kootenai River, which originates in British Columbia, Canada, flows through Montana and Idaho before returning to British Columbia and entering Kootenay Lake. The Kootenai River provides an excellent opportunity to apply a remotely sensed macrophyte characterization approach to a riverine system where current research is ongoing. We plan to fly the 75-kilometer stretch of the Kootenai River in Idaho, from just west of Bonners Ferry to the Canadian border, which includes the main deep, slow-moving meander section, islands, and engineered structures. Our analysis will be conducted using a Wingtra Gen II fixed-wing UAV with the Micasense RedEdge-P multispectral imager at 2–4 m spatial resolution in the visible and near-infrared bands. The planned data acquisition will be conducted during a low-flow period, thereby maximizing the penetration depth of the imaging sensor into the water. Initial analysis of the USGS National Agricultural Imagery Program (NAIP) 2023 VNIR imagery demonstrated that a remote-sensing approach can detect SAV along the Kootenai River at 1 m spatial resolution. SAV was found in areas where water movement was reduced, or the depth became shallower, such as near islands, point bars, backwaters, and man-made structures. The initial NAIP classification using 1-meter imagery will enable us to optimize the Wingtra Drone flight plan, reducing collection, processing, and analysis time and costs. Food resource availability in large oligotrophic rivers is crucial for supporting higher trophic levels, as these environments are inherently nutrient-poor and biomass-limited. Mapping the distribution of macrophyte assemblages at this scale provides cost-effective and timely information to support river management decisions.