The leather industry is a major source of environmental pollution in India. The wastewater generated by leather industries contains very high pollution parameters due to the presence of a complex mixture of organic and inorganic pollutants even after the treatment at a Common Effluent Treatment Plant (CETP) and disturbs the ecological flora and fauna. The nature, characteristics and toxicity of CETP treated wastewater is yet to be fully elucidated. Thus, this study aims to characterize and evaluate the toxicity of CETP treated tannery wastewater collected from the Unnao district of Uttar Pradesh, India. In addition to measuring the physico-chemical parameters, the residual organic pollutants was identified by GC-MS analysis and phytotoxicity, cytotoxicity and genotoxicity of the treated wastewater was evaluated using Vigna radiata L. and Allium cepa L. Results showed that the treated wastewater contained very high pollution parameters (TDS 3850 mg/L, BOD 680 mg/L, COD-1300 mg/L). GC-MS analysis revealed the presence of various types of residual organic pollutants including benzoic acid, 3-4,-(T-butyl) Phenyl furan-2-5-dione, benzeneacetamide, resorcinol, dibutyl phthalate, and benzene-1,2,4-triol. Further, toxicological studies showed the phytotoxic nature of the wastewater as it inhibited seed germination in V. radiata L. and root growth of A. cepa. Genotoxicity was evidenced in the root tip cell of A. cepa where chromosomal aberrations (stickiness, chromosome loss, C-mitosis, and vagrant chromosome) and nuclear abnormalities like micronucleated and binucleated cells were observed. Thus, results suggested that it is not safe to discharge these wastewater into the environment. Display omitted •Tannery wastewater rich in organic and inorganic pollutants.•Tannery wastewater possesses genotoxic and cytotoxic pollutants.•Phytotoxic nature of tannery wastewater was evaluated by Vigna radiata seeds.•Allium cepa chromosomal tests revealed genotoxic nature of treated tannery wastewater.•Wastewater also induced chromosomal aberrations and nuclear abnormalities in cells.