The safe disposal of pulp and paper mill effluent is still a threat to the environment due to the presence of several unknown organic pollutants. The comparative physico-chemical analysis of pulp and paper mill effluent-contaminated sediment (PPECS) of site 1 and site 2 showed that the sediment had an alkaline nature and was loaded with several organic pollutants and heavy metals. SEM-EDX examination showed a porous structure with a heterogeneous distribution of particles, allowing the adsorption of metal and other complex organic ions. FTIR analysis depicted the presence of a variety of functional groups, i.e., alkyl halides, phenolics, and lignin, in the contaminated sediment. GC-MS analysis showed the major presence of organic pollutants, i.e., 2-methyl-4-keto-2-pentan-2-ol and 3,7-dioxa-2,8-disilanonane,2,2,8,8-tetramethyl-5-[(trimethylsilyl)oxy], in the site 1 sediment contaminated with pulp and paper mill waste, while 2-methyl-4-keto-2-trimethylsiloxypentane, 4-ethyl-2-methoxyphenol, ethyl-2-octynoate, cis-9-hexadecenoic acid, and octadecenoic acid were detected in the site 2 sediment contaminated with pulp and paper mill waste. The genotoxicity of PPECS determined by examining Allium cepa root cell division showed chromosomal aberration. In this study, several compounds that have not been reported before were identified.