The effectiveness of mine-waste remediation at the Clark Fork River Superfund site in western Montana, USA, was examined by monitoring metal concentrations in resident biota (caddisfly, Hydropsyche spp.) and bed sediment over a 19-year period. Remediation activities began in 1990 and are ongoing. In the upper 45 km, reduced Cu and Cd concentrations at some sites were coincident with remediation events. However, for a period of three years, the decline in Cu and Cd directly below the treatment ponds was offset by high arsenic concentrations, suggesting that remediation for cations (e.g., Cu and Cd) mobilized anions such as arsenic. The impact of remediation in the middle and lower reaches was confounded by a significant positive relationship between metal bioaccumulation and stream discharge. High flows did not dilute metals but redistributed contaminants throughout the river. The majority of clean-up efforts were focused on reducing metal-rich sediments in the most contaminated upstream reach, implicitly assuming that improvements upstream will positively impact the downstream stations. We tested this assumption by correlating temporal metal trends in sediment between and among stations. The strength of that association (r value) was our indicator of spatial connectivity. Connectivity for both Cu and Cd was strong at small spatial scales. Large-scale connectivity was strongest with Cu since similar temporal reductions were observed at most monitoring stations. The most upstream station, closest to remediation, had the lowest connectivity, but the next three downstream sites were strongly correlated to trends downstream. Targeted remediation in this reach would be an effective approach to positively influencing the downstream stations.