The development of hydropower in the St. Marys River (SMR) in the early 1900s led to the construction of the 16-gate Compensating Works, approved by the International Joint Commission, to regulate water levels in Lake Superior and Lake Huron. These gates are adjusted monthly to accommodate seasonal water levels in the upper Great Lakes, causing rapid changes in flow and water levels in the SMR Rapids, a critical habitat for fishes and benthic macroinvertebrates. Despite over a century of operation, the ecological effects of these gate operations remain largely unknown. Therefore, the objectives of our study are to: (1) determine the extent of stranding of fish, fish eggs, and benthos due to gate closures, and (2) evaluate the extent of flushing of riverine biota during gate openings. Over the past year, we conducted three gate closure surveys (0.5 to 4 gates closed) and five gate opening surveys across different gate operation conditions. Preliminary results indicate that gate closures exposing >800 m2 of habitat cause significant mortality of fish, crayfish, and benthic macroinvertebrates. In each survey, over 100 stranded fish were observed, including species such as Cottus bairdii, Onchorhynchus mykiss, and Onchorhynchus tshawytscha, alongside high densities of macroinvertebrates. During gate openings, when flow rapidly increases, no significant change in drift was detected downstream of the Rapids. Our findings suggest that gate operations may be causing unintended ecological impacts to a habitat that supports a highly valuable recreational fishery. Given the variability in gate operations, seasonal timing, and gate combinations, further research is needed to refine flow management strategies that minimize ecological loss while maintaining water regulation objectives.