There is considerable interest in evaluating the status and trends of sturgeon populations, yet many traditional approaches to estimating the abundance of fishes are intractable due to their biology and rarity. Side-scan sonar has recently emerged as an effective tool for censusing sturgeon in rivers, yet challenges remain for censusing open populations that may visit specific habitats over periods of time (e.g., spawning runs). We use a hierarchical model to integrate side-scan sonar with acoustic telemetry, to estimate the proportion of a spawning run fitted with acoustic tags (12%; 95% CRI = 8-16%) and extrapolate to the total run size in 2014. Our investigation represents a novel approach to generating run size estimates in a large river and provides the first estimate of Atlantic sturgeon spawning run size for the Hudson River (N ̂ = 466; 95% CRI = 310-745) since the fishery moratorium in the 1990’s. Our estimate suggests that the Hudson River holds one of the largest contemporary populations of Atlantic sturgeon, but also indicates that it remains sharply depleted relative to virgin conditions.