A legacy of hard rock mining has historically impaired the ecological health of the upper Clark Fork Basin (Montana, USA). Since the Superfund designation in the 1980s, large stretches of the upper Clark Fork River and its tributaries have been restored, leading to improvements in water quality and fish populations. However, in the last decade, nearly all three-year-old or younger brown trout have been absent from the most upstream reach of the Clark Fork River, from below Warm Springs to Galen. To better understand metal-related risks to aquatic life, we evaluated metal(loid) (arsenic, cadmium, copper, lead, zinc) concentrations and loads. Assessments looked across four sites in the upper Clark Fork Basin with varying degrees of restoration, exposure to active and historical mine wastes, and fish population histories. Flow-normalized trends in metal concentrations and loads were estimated using the Weighted Regressions on Time, Discharge, and Season model. Annual average concentrations of most metal(loid)s have declined over nearly 30 years, with the largest declines at restored sites and smallest declines at unrestored sites. For example, from 1997 to 2024, total copper concentrations declined by 91% at Silver Bow at Opportunity (restored) yet only 16% at Clark Fork at Deer Lodge (unrestored). Despite declines in metal(loid) concentrations, all sites still commonly exceed chronic water quality criteria that are protective of aquatic life. Concentration-discharge analysis and differences in loads among sites suggest that restoration is effective at reducing the source of copper available for transport to the river. However, upstream improvements due to restoration are not translated to downstream unrestored sites because the restored sites contributed only 12% of the total copper load at the most downstream site (Clark Fork at Deer Lodge) between 2019 and 2024. These results suggest arsenic, cadmium, copper, lead, and zinc concentrations may not be related to the decline in fish populations, but are a persistent stressor to aquatic life, especially in reaches that have yet to be restored.