Continued study of the relationship between lake sturgeon (Acipenser fulvescens) recruitment and hydroelectric dams and operations, in a variety of river systems and habitat types is needed to improve the ability to predict and monitor impacts of the hydroelectric industry on this species. Herein, we present results of a juvenile lake sturgeon study aimed at addressing concerns over an inferred lack of recruitment resulting from spawning downstream of a hydroelectric generating station (HGS). Two years of sampling (2015 and 2016) were conducted in five sections of a 41 km long reach of the Seine River, Ontario, a lake sturgeon spawning tributary of Rainy Lake. Using an established gillnetting method, deepwater habitat was targeted to capture juvenile lake sturgeon to assess relative abundance, recruitment (cohort strength), and growth. Deepwater habitat, defined as water depths >6 m in this system, comprised only 2.1% of the wetted area in this study area. Within these habitats, a total of 331 lake sturgeon capture events were observed over the 2‐years study period. The majority of the lake sturgeon catch (85%) was comprised of age‐0 to age‐5 individuals (both sampling years combined). Although inter‐annual variation in cohort strength was apparent, each cohort between 2006 and 2016 was represented. The spatial distribution of cohorts varied among river reaches with younger individuals (age‐0 and age‐1) occupying reaches proximal to the Sturgeon Falls HGS, and larger, older individuals (age‐2 to age‐5) occupying reaches further downstream. The rarity of age‐6+ individuals can likely be explained by ongoing downstream redistribution of juveniles over time, out of the Seine River and into Rainy Lake. Growth of juvenile lake sturgeon captured in the Seine River was above average relative to conspecifics from other rivers in the Hudson Bay drainage. Unfortunately, baseline data sets required to facilitate comparisons of contemporary (post‐construction Sturgeon Falls HGS) versus historical (i.e. pre‐ Sturgeon Falls HGS) lake sturgeon recruitment, or to evaluate the influence of the Seine River Water Management Plan (2004) on lake sturgeon recruitment, are lacking. However, juvenile Lake Sturgeon are more abundant in this system than what had been surmised based on recent studies which implemented random sampling. Results indicate that juvenile lake sturgeon may reside in spawning tributaries for several years (age‐0 to age‐5) prior to seeking alternate habitats and highlights the value of targeted sampling (i.e. by depth) along the flow axis of rivers downstream of spawning areas when assessing lake sturgeon recruitment patterns.