The Lower Duwamish River is a highly industrialized waterway flowing into the densely urbanized Puget Sound waterfront of Seattle, Washington, USA. The river has been profoundly altered from its natural state following more than a century of channelization, recurrent dredging, shoreline armoring, and pollution discharges. As part of a Natural Resource Damage Assessment addressing historical pollution at three designated Superfund sites (i.e., the assessment area), juvenile Pacific staghorn sculpin (Leptocottus armatus) were sampled throughout the lower river in order to evaluate injury from exposure to polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethane (DDTs), and butyltins (BTs). Sculpin live in close association with the river sediments within and upriver of the assessment area. Fish were collected for analysis of contaminant concentrations in composited whole bodies and stomach contents, as well as individual fish health metrics including daily somatic growth rates measured from otoliths. Sediment contaminant concentrations were also measured at sites near to fishing locations. Fish growth rates varied from 0.65 to 1.05 mm/day, and were significantly lower at unremediated downriver sites compared to upriver and remediated locations. Sculpin growth rates were negatively correlated with concentrations of PCBs in fish bodies, PAHs in stomach contents, as well as PCBs, DDTs and PAHs in sediment. Mixed effects models for whole-body and stomach content contaminants showed positive correlations between growth rate and water temperature. Temperature was not a significant confounding variable for the relationship between growth rate and sediment contaminants. Overall, these results show that juvenile sculpin are harmed by contaminant exposure in the Lower Duwamish River. Furthermore, this study demonstrates the utility of using paired biological and chemical indicators of pollutant-induced injury in a resident fish to inform a complex Natural Resource Damage Assessment and associated restoration efforts.