Sediment chemistry and arcellacean community composition were analyzed to study the ecological effects of copper mine-derived acidic and metal-rich waters in a freshwater bay in eastern Finland. To track spatial and temporal changes in the bay, 32 mine-impacted (top) and pre-impact (bottom) samples were analyzed from 16 short sediment cores taken along a transect extending from the pollution source. In addition, short cores from the impacted and reference sites were studied. Recent sediments displayed a geochemical gradient from the inner bay, where mine water is discharged, to the outer bay. Inner bay sites were enriched with C, S, and Fe, whereas Mn was depleted, but has precipitated in the outer bay. Among the heavy metals, Cu, Al, Zn, and Ni concentrations had increased in the inner and mid bay, while Co and Cd concentrations had increased at mid-bay sites. The change from the natural to mine-impacted condition was also seen in faunal gradients. According to ordination and distance measures, the greatest changes in species composition occurred in the inner bay, with fairly small changes in the outer bay. Numerical methods suggested that metals (Cu, Pb, Al, Zn, Cr), redox-sensitive elements (Fe, Mn), organic carbon and nutrients could be related to changes in arcellacean assemblages. Geochemical changes in the impacted core started at ~20 cm with increases in S alternating with peaks in Cr and Mg. Heavy metal concentrations increased markedly at 10 cm, after the active mining period, suggesting the beginning of acid mine drainage. Geochemical changes at ~20 cm were already apparent in the arcellacean assemblages, but the most notable change coincided with the geochemical shift at 10 cm, with signs of decreased pH. Numerical methods suggest that mining-related metals Co, Cu, Zn and Ni co-vary with arcellaceans, but Al appears to behave independently with respect to the species data. ©2009 Springer Science+Business Media B.V.