Buriganga, an economically important river of Dhaka, Bangladesh, is highly polluted by different toxic heavy metals. In this study, phytoremediation of EMS induced Indian mustard (Brassica juncea L) genotypes against three pollutants viz. lead (Pb), chromium (Cr) and cadmium (Cd) of Buriganga riverbank soil was assessed in field condition. Among 1-, 2- and 3% EMS induced genotypes, better seed germination rate, germination speed and plant survival rate were observed in 1% EMS induced genotype, BE21. The highest concentration of Pb, Cr and Cd were also obtained in the leaf of BE21 genotype and therefore was considered as a super-hyperaccumulator genotype. Concentration of Pb in the next generation of this genotype was approximately two-fold higher in the root (91.53 mg/kg dry weight, DW); three-fold higher in the shoot (33.31 mg/kg DW) and leaf (28.35 mg/kg DW), and more in the fruit (5.59 mg/kg DW) than the control. Concentration of Cr was approximately two-fold in the root (57.02 mg/kg DW), shoot (18.51 mg/kg DW) and leaf (14.98 mg/kg DW), and more in the fruit (6.15 mg/kg DW) of BE21 genotype compared to the control. Cd concentration was more in the root (1.96 mg/kg DW), leaf (0.52 mg/kg DW) and fruit (0.19 mg/kg DW) and less in the shoot (0.19 mg/kg DW) of BE21 genotype than the control. Root, shoot, leaf and fruit of BE21 altogether accumulated 98-, 73- and 87% Pb, Cr and Cd, respectively and can thus be utilized to remove heavy metals of Buriganga River. As like root, shoot and leaf, fruit also accumulated heavy metals; hence those plants which are used in phytoremediation should not be used as food or fodder. To the best of our knowledge, this is the first report of developing EMS induced hyperaccumulator genotype of B. juncea for phytoremediation of Buriganga riverbank soil of Bangladesh.