Mineralogical characterization by X-ray diffraction (XRD) and a high throughput automated quantitative evaluation of minerals by scanning electron microscopy (QEMSCAN) was conducted on samples from a sulphate-reducing biochemical reactor (BCR) treating high concentrations of metals (As, Zn, Cu) in smelter waste landfill seepage. The samples were also subjected to energy dispersive X-ray (EDX) analysis of specific particles. The bulk analysis results revealed that the samples consisted mainly of silicate and carbonate minerals. More detailed phase analysis indicated four different classes: zinc-arsenic sulphosalts/sulphates, zinc-arsenic oxides, zinc phosphates and zinc-lead sulphosalts/sulphates. This suggests that sulphates and sulphides are the predominant types of Zn and As minerals formed in the BCR. Sphalerite (ZnS) was a common mineral observed in many of the samples. In addition, X-ray point analysis showed evidence of As and Zn coating around feldspar and amphibole particles. The presence of arsenic-zinc-iron, with or without cadmium particles, indicated arsenopyrite minerals. Copper-iron-sulphide particles suggested chalcopyrite (CuFeS 2 ) and tennantite (Cu,Fe) 12 As 4 S 13 . Microbial communities found in each sample were correlated with metal content to describe taxonomic groups associated with high-metal samples. The research results highlight mineral grains that were present or formed at the site that might be the predominant forms of immobilized arsenic, zinc and copper.