The copper refinery process produces Se(VI)-bearing wastewater with a high content of Cl<sup>−</sup> and SO<sub>4</sub><sup>2−</sup> ions. To overcome the negative effect caused by Cl<sup>−</sup> and SO<sub>4</sub><sup>2−</sup> ions on Se(VI) reduction and its following removal, this study investigated the possible synergistic effect of the combination of Se(VI)-reducing bacterium, <i>Thaurea</i> (<i>T.</i>) <i>selenatis</i> and zero-valent iron (ZVI). In the presence of SO<sub>4</sub><sup>2−</sup> (200 mM) and Cl<sup>−</sup> (300 mM), the following was observed: (i) ZVI alone was unable to remove Se both under strictly aerobic and micro-aerobic conditions. (ii) Se(VI) reduction by <i>T. selenatis</i> alone was severely inhibited under anaerobic conditions (and thus no microbial growth was observed). (iii) On the other hand, <i>T. selenatis</i> was capable of growth and Se(VI) reduction under micro-aerobic conditions. (iv) Combining <i>T. selenatis</i> and ZVI under micro-aerobic conditions showed a synergistic effect on Se(VI) reduction, readily facilitating Se removal. This synergistic effect was optimized by adjusting the pH to near neutral (optimal for <i>T. selenatis</i> growth), but by adjusting the temperature to 35°C (sub-optimal for <i>T. selenatis</i> growth): Se removal of 55% by <i>T. selenatis</i> alone, was significantly improved to 98% by combining <i>T. selenatis</i> and ZVI. The proposed key process to display the synergistic effect on Se removal under micro-aerobic conditions is as follows: (i) Using the remaining dissolved O<sub>2</sub> (DO) during the first hours, <i>T. selenatis</i> can overcome the inhibitory effect of Cl<sup>−</sup> and SO<sub>4</sub><sup>2−</sup> by growing with more energy-gaining aerobic respiration, (ii) ZVI indirectly serves as a reducing agent to maintain low DO levels, consequently readily switching from aerobic to anaerobic Se(VI) respiration by <i>T. selenatis</i>. (iii) ZVI may also be acting directly for Se deposition by reducing microbially-produced intermediate Se(IV), which is more reactive than original Se(VI). The present findings could be used as a basis for developing an economically feasible and environmentally harmless bio-treatment technology for Se(VI) containing copper refinery wastewaters.