Summary Adaptive management and recovery initiatives for long-lived, late-maturing species such as Lake Sturgeon, Acipenser fulvescens, are complicated by temporal lags. By the time anthropogenic impacts on critical periods (spawning, larval hatch, age-0 survival) would be manifested in adult populations, decades might have passed. However, recruitment patterns and population trajectory responses (both positive and negative) can be identified by examining the juvenile life stage. This study describes and evaluates a gill net method for sampling juvenile Lake Sturgeon between 250 and 800 mm fork length (FL) resident in Boreal Shield rivers in relative proportion to their abundance. The method is based on previous observations of deepwater preference (>10–15 m), and employs mesh sizes of 25.4, 50.8, 76.2, 127.0 and 152.4 mm stretched measure. Selectivity curves were generated based on 1040 Lake Sturgeon captures from six reaches of the Winnipeg and Nelson rivers, Canada. A normal (common spread) curve approximated a normal distribution centered on ~390 mm FL, and relative selection exceeded 0.65 across the 250–800 mm FL range. For the Slave Falls Reservoir (Winnipeg River), Spearman's rank-order correlation (ρ) for zone-specific cohort-frequency distributions in adjacent sampling years ranged from 0.85 to 0.93, while the score for the entire reservoir was 0.95, suggesting inter-annual consistency. The method allows for rapid and robust assessments of relative abundance and cohort strength for juvenile Lake Sturgeon within large Boreal Shield river systems, and facilitates biological comparisons among reaches and over time. Incidentally, cohort frequency results derived herein indicate that juvenile recruitment in regulated Boreal Shield rivers can be erratic, irrespective of size of the spawning stock. Such a pattern could be an inherent characteristic of the species that needs to be accounted for when developing adaptive management and species recovery plans.