We subjected a unique set of high-quality paleoecological data to statistical modeling to examine if the biological richness and evenness of freshwater diatom communities in the Falun area, a historical copper (Cu) mining region in central Sweden, was negatively influenced by 1000 years of metal exposure. Contrary to ecotoxicological predictions, we found no negative relation between biodiversity and the sedimentary concentrations of eight metals. Strikingly, our analysis listed metals (Co, Fe, Cu, Zn, Cd, Pb) or the fractional land cover of cultivated crops, meadow, and herbs indicating land disturbance as potentially promoting biodiversity. However, correlation between metal- and land-cover trends prevented concluding which of these two covariate types positively affected biodiversity. Because historical aqueous metal concentrations-inferred from solid-water partitioning-approached experimental toxicity thresholds for freshwater algae, positive effects of metal mining on biodiversity are unlikely. Instead, the positive relationship between biodiversity and historical land-cover change can be explained by the increasing proportion of opportunistic species when anthropogenic disturbance intensifies. Our analysis illustrates that focusing on the direct toxic effects of metals alone may yield inaccurate environmental assessments on time scales relevant for biodiversity conservation.