Abstract • An innovative bubble column tower BPE was designed to treat the black-odorous water. • PO43−, S2− and turbidity were removed, and dissolved oxygen was enriched in the BPE. • An aluminum bipolar electrode gave the best oxygen enrichment and pollutant removal. • Changes of microorganisms confirmed the improvement in water quality achieved. The large amount of municipal wastewater discharged into urban rivers sometimes exceeds the rivers’ self-purification capacity leading to black-odorous polluted water. Electro-flocculation has emerged as a powerful remediation technology. Electro-flocculation in a bubble column tower with a bipolar electrode (BPE) was tested in an attempt to overcome the high resistance and weak gas-floatation observed with a monopolar electrode (MPE) in treating such water. The BPE reactor tested had a Ti/Ta2O5-IrO2 anode and a graphite cathode with an iron or aluminum bipolar electrode suspended between them. It was tested for its ability to reduce turbidity, phosphate and sulphion and to increase the concentration of dissolved oxygen. The inclusion of the bipolar electrode was found to distinctly improved the system’s conductivity. The system’s electro-flocculation and electrical floatation removed turbidity, phosphate and sulphion completely, and the dissolved oxygen level improved from 0.29 to 6.28 mg/L. An aluminum bipolar electrode performed better than an iron one. Changes in the structure of the microbial community confirmed a significant improvement in water quality.