This is the first successful report on selenium bio-attenuation to satisfy drinking water regulations as per Indian Standards (10 μg/L) in the presence of concomitant nitrate and sulfate from water sources utilizing a fixed bed bioreactor. The bioreactor was immunized with blended microbial culture and worked in downflow mode under anoxic conditions at 30 ± 2 °C for around 190 days under varying influent selenate (100–500 μg/L as selenium), nitrate (50 mg/L), sulfate concentrations (as per selenium removal) and necessary dose of acetic acid (as COD, a carbon source) in synthetic groundwater, operated at an empty bed contact time (EBCT) of 45–120 min. After supplying an adequate dosage of sulfate and alteration of EBCT, selenium was found to comply with drinking water regulations and nitrate was completely removed. X-ray diffraction and transmission electron microscopy analyses depicted nanocrystalline selenium sulfides (SeS and SeS2) formation as the possible mechanisms of selenium removal. Extended toxicity characteristic leaching procedure (TCLP) extractions confirmed a maximum selenium leaching of 52 and 282 μg/L during anoxic and oxic extractions, respectively. Long-term column leaching (>3-month equilibration) under aerobic conditions at pH 7 confirmed the produced precipitate to be essentially stable (∼0.14% Se leaching). This work exhibits the synchronous bioremoval of selenium and its co-anions from contaminated water complying with drinking water standards, and leaving a stable and non-hazardous selenium-laden biosludge.