The study probed into reducing faecal indicators and pathogenic bacteria, heavy metals and β-lactam antibiotics, from four types of secondary effluents by bioaugmentation process, which was conducted with Bacillus subtilis strain at 45 °C. As a result, faecal indicators and pathogenic bacteria were reduced due to the effect of thermal treatment process (45 °C), while the removal of heavy metals and β-lactam antibiotics was performed through the functions of bioaccumulation and biodegradation processes of B. subtilis. Faecal coliform met the guidelines outlined by WHO and US EPA standards after 4 and 16 days, respectively. Salmonella spp. and Staphylococcus aureus were reduced to below the detection limits without renewed growth in the final effluents determined by using a culture-based method. Furthermore, 13.5% and 56.1% of cephalexin had been removed, respectively, from secondary effluents containing 1 g of cephalexin L−1 (secondary effluent 3), as well as 1 g of cephalexin L−1 and 10 mg of Ni2+ L−1 (secondary effluent 4) after 16 days. The treatment process, eventually, successfully removed 96.6% and 66.3% of Ni2+ ions from the secondary effluents containing 10 mg of Ni2+ L−1 (secondary effluent 2) and E4, respectively. The bioaugmentation process improved the quality of secondary effluents.