Toxicity of AMD on rice seedlings lead to abnormal growth and development. Concentration (mg/L) of Mn (1671.17), Cu (84.55), Al (4530), Ti (834.97), Si (1974), S (1028) and Fe (12462) were detected in AMD. We developed an integrated bacteria-algal technology efficiently removing >95% of toxic metals from AMD after 48 h of treatment following microalgae culture for rising DO from 3.78 to 6.7 mg/L. Germination (%) of rice seed was found to be maximum with detoxified AMD and control condition showing 94.55% and 94.44% respectively whereas 53.32% of germination was with AMD. Catalase activity (U/mg/min) and peroxidase activity (U/mL) were found as 80.52 < 90.10 < 127.93 < 152.59 and 2.18 < 2.46 < 2.60 < 3.36 respectively with control, detoxified AMD, AMD, and CuSO4.5H2O. Genotoxicity of treated AMD was found to be negligible in comparison to AMD on root cells of rice seedlings.