The St. Marys River (SMR) forms the border between Michigan, USA, and Ontario, Canada, connecting lakes Superior and Huron. Discharge is controlled by a 16-gate water control structure upstream of the SMR rapids. The SMR rapids are a critical spawning habitat in the Great Lakes, yet the influence of regulated discharge on larval fish export remains poorly understood. From 2018 to 2021, larval fish were sampled across four locations to assess community composition and export dynamics under varying discharge releases. Rainbow smelt (Osmerus mordax) dominated catches (87.9 %), followed by species in the family Leuciscidae (i.e., native minnows) and burbot (Lota lota). Larval densities were strongly influenced by water temperature and, to a lesser extent, discharge. Bayesian state-space models estimated a total export of ∼ 41.3 million larvae from the rapids across 3 years, with the highest export in 2019. Rainbow smelt larvae exhibited peak densities at intermediate flows (300–600 m³ s⁻¹) and temperatures (∼18–19 °C), while non-rainbow smelt taxa showed species-specific, less consistent responses. Nighttime sampling consistently yielded higher larval densities. Export estimates varied by analysis but both manual and Bayesian approaches captured similar interannual and taxonomic trends. Despite past expectations, the larval community was largely composed of prey species, with limited representation of lake sturgeon (Acipenser fulvescens), lake whitefish (Coregonus clupeaformis), or walleye (Sander vitreus). These results suggest the SMR rapids currently support significant forage fish production and highlight the importance of discharge and temperature in structuring larval export.