Sequencing batch reactor (SBR) is useful in removal of both non-biodegradable and biodegradable contaminants from wastewater. The main aim of the present investigation was to evaluate the potential of biocatalyst strain RA-14 on heavy metal removal under SBR. The selected strain was screened from the soil sediment contaminated with heavy metals. It was able to survive at different (Hg²⁺, Pb²⁺, Zn²⁺, Cu²⁺, Cd²⁺ and Ni²⁺) heavy metals (>500 ppm). The bacterial strain RA-14 showed maximum bioaccumulation potential than other strains. Heavy metal resistance patterns of Pb²⁺ > Cu² > Cd²⁺ > Hg²⁺, Ni²⁺ and Zn² was observed. Strain RA-14 was resistant to penicillin–G, nalidixic acid, ceftazidime, cefotaxime, kanamycin and ampicillin. The results revealed that bioaccumulation activities were improved at pH 7.0 (83.2 ± 1.8%), 40 °C (89.34 ± 3%) and affected at higher pH values and temperature. The results showed that contact time and initial Lead concentration was also affected Lead accumulation. The heavy metal tolerant strain RA-14 was further investigated towards heavy metal removal in SBR. Heavy metal was removed in SBR within 10 h of hydraulic retention time. Heavy metal removal was high at 2 mg/L (0.33 mg/L Cu²⁺, 0.33 mg/L Hg²⁺, 0.33 mg/L Pb²⁺, 0.33 mg/L Zn²⁺, 0.33 mg/L Cd²⁺ and 0.33 mg/L Ni²⁺) heavy metals. Total nitrogen, biological oxygen demand (BOD) and chemical oxygen demand (COD) of treated water in SBR was removed and the removal efficacy was 91.3 ± 2.1%, 97.6 ± 3.3%, and 94.3 ± 4.4%, respectively in 10 h hydraulic retention time. However, the efficiency of BOD, COD and total nitrogen content removal was decreased, due to the reduced metabolic process of bacteria after 10 h. The SBR reactor proved to be an efficient method for the treatment of various heavy metals from the wastewater.