Temporal monitoring studies are needed to detect long-term trends in ecosystem health. In the present study, we tested metallothionein (MT) as a potential biomarker for long-term variations in trace metal levels in lakes subject to atmospheric metal inputs from a nearby copper smelter. Over a 13-year period, we estimated on several occasions ambient free Cd2+, Cu2+ and Zn2+ concentrations at the sediment-water interface in six lakes with contrasting metal levels, and measured metal and metallothionein concentrations in gills of bivalves (Pyganodon grandis) living in these lakes. All but one of the study lakes had comparable drainage ratios, so inter-lake differences in hydrological export of metals from contaminated watersheds to receiving waters were likely minimal. Declines in the metal emissions from the smelter (especially for Cd and Zn) during the 1980s led to appreciable decreases in both calculated free Cd2+ ion concentrations in the study lakes (-59+/-21% between 1989 and 1998) and accumulated Cd levels in their clam populations (-46+/-12% between 1989 and 2002). Taking all lakes into account, MT concentrations in bivalves have comparatively dropped by 44% (+/-10%) since 1989. In contrast to what we found for Cd, there were no significant reductions in the calculated free Cu2+ and Zn2+ concentrations in the various lakes during our study period (-2 and -10%, respectively, with 95% confidence intervals spanning zero). Overall, observed decreases in MT in bivalves over time were best correlated with similar decreases in both ambient and accumulated Cd levels (r = 0.77, P = 0.0003 and r = 0.79, P < 0.0001, respectively, both P-values corrected for temporal autocorrelation), suggesting that long-term trends in gill MT concentrations in P. grandis may be useful as predictors of temporal changes in environmental Cd contamination in lakes.