Allchar ore deposit, a well-known polymetallic mineralisation, is drained by the Majdanska River characterized by elevated concentrations of heavy metals and metalloids, particularly As, Tl and Sb. The present study was conducted at the spot of the confluence of spring water, heavily loaded with toxic metals, which joins the Majdanska River by a few meters short stream. The spring water is outflow of underground water drained by passage through polymetallic mineralisation. The chemical characteristics of the Majdanska River water and the associated periphyton were used to evaluate and explain the abiotic response to the intrusion of toxicants and its impact on biota. At the site of the stream inflow, thorough mixing of Majdanska River water and incoming spring water resulted in an increase of Eh and pH close to the average river value. This geochemical barrier causes significant changes in the mobility of metal species. Moreover, the output composition of water is further modified by biological processes. The examined biota community was found to consist of algae Audouinella sp. and Spirogyra sp., with coexisting freshwater snails Radix labiata, diatoms and bacteria. While the carbonate bedrock controls the pH of the river water by effective buffering, it seems that bioconcentration and biomineralisation of algae exerted control on toxicants along the entire river flow. The highest bioconcentration factors were obtained for Fe, Mn and Ti which implies the biomineralisation of iron as a product of extracellular deposition on the cell walls on the organic matrices. Bioconcentration of As, Cr, Cs, Cu and Se was more important in Audouinella sp., while Cd, Co, Sr, and Zn preferentially accumulated in Spirogyra sp. High accumulation of Ba (3 mg/g d.w.) in Spirogyra sp. was associated with the intracellular biomineralisation. These findings suggest the potential use of Spirogyra sp. in the remediation of waters polluted by barium or as the biological pathfinder indicator for metal deposits associated with barite.