The mainstem of large, channelized, and regulated rivers are often referred to as sterile halfpipes with reduced biological diversity. However, these reaches may contain more complexity and ecological activity than is initially apparent. Macrophyte assemblages can influence hydrology, substrate stability, and organic matter retention, which can influence macroinvertebrate abundance. Yet, in regulated systems, the extent to which macrophyte community structure mediates resource availability remains poorly understood. Understanding habitat characteristics that influence fish and prey distribution across trophic levels is critical for effective management. Macrophytes provide essential nutrients, cover, and substrate for macroinvertebrates and juvenile fish, which, in turn, serve as prey for larger piscivores. This study will quantify macrophyte distribution, diversity, and native versus non-native composition throughout the meander section of the Kootenai River between Bonners Ferry and Porthill, Idaho (~75 river kilometers). This section is characterized by slower flow velocities (0.17 m/s−1) and deeper water (~6.4 m) compared to upstream reaches. Preliminary observations indicate macrophytes accumulate along shallow shorelines and near islands, potentially creating productive foraging areas. Fish have also been found to accumulate near islands, suggesting that island features may create gradients of productivity. As such, sampling will focus on habitats associated with islands, backwater areas, and representative mainstem shorelines, allowing us to capture spatial distribution. Standard rake sampling methodology will be used to collect macrophytes for characterization. Macroinvertebrates associated with macrophytes will be collected and identified to the family level. We will compare macroinvertebrate abundance, diversity, and functional feeding group composition associated with native, non-native, emergent, and submersed macrophytes. We hypothesize that native macrophytes will support more abundance and diversity of macroinvertebrates. Identifying productive refugia will inform management strategies and restoration priorities aimed at enhancing nutrient and prey availability in an oligotrophic river and similar systems. By linking macrophyte community structure and macroinvertebrate diversity, we will highlight localized biodiversity hotspots that may serve as critical food resources. This challenges the notion that large river mainstems are uniformly unproductive.