The Clark Fork River (Montana, USA) is a major tributary of the Columbia River with more than a century of copper mining in the Clark Fork River Basin (basin) that has resulted in metal contributions, impacting both stream ecosystems and public water supplies. Sediment from metal-enriched waste rock is the largest source of metal loads in the Clark Fork River and has been transported more than 121 km downstream from the mines. As a result of mining legacies, the basin contains the largest contiguous complex of Federal Superfund sites in the United States. Remediation efforts in the basin began in 1990 and are currently ongoing. Significant efforts include the creation of tailing ponds to capture metal-rich sediment from travelling downstream and removal of tailings from the basin, resulting in changes to downstream sediment transport. While concentrations of metals in the water column have declined sharply at some sites over the past decades, recent studies have found that once recovered trout populations are again nearly extirpated from portions in the upper river basin. To investigate how remediation influences metal accumulation, the U.S. Geological Survey began collecting sediment and aquatic invertebrate samples across the upper Clark Fork River in 1986. We analyzed this multi-decadal record and found that concentrations of arsenic, iron, and manganese were lower in tissues of predatory macroinvertebrates compared to those of filter feeders. In certain upstream sites, metal concentrations have also been observed to decrease in sediment and insect tissues since restoration began. These findings suggest that metal accumulation might have trophic-specific pathways, even withstanding long term trends of decreasing metal concentrations. Further research aims to quantify the transport of metals from sediment into food webs and how that may be influenced by spatiotemporal patterns of mining-related contaminants across the basin.