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Sediment samples collected from the river Shitalakhya, Bangladesh, were analyzed using atomic absorption spectroscopy (AAS) to investigate site-to-site (spatial) and seasonal (i.e., dry, pre-monsoon, post-monsoon) variation of Cr, Mn, Ni, Cu and Zn. The mean concentrations of Cr, Mn, Ni, Cu and Zn were 22.37 ± 6.09, 612.59 ± 160.08, 54.11 ± 11.21, 50.36 ± 9.40 and 103.62 ± 62.74 mg/kg in the dry, 31.58 ± 5.22, 569.71 ± 112.16, 58.35 ± 7.82, 49.93 ± 17.36 and 110.88 ± 95.83 mg/kg in the pre-monsoon and 18.09± 6.32, 567.02 ± 115.55, 50.89 ± 6.58, 39.75 ± 4.56 and 55.22 ± 11.33 mg/kg in the post-monsoon, respectively. Based on the metals’ concentrations, no considerable difference was observed among the three seasons, but the concentrations were slightly elevated in the dry and pre-monsoon compared to that in the post-monsoon with respect to site-to-site variation. Among the metals examined, concentrations of Ni and Cu were elevated because of the use of oxides of these heavy metals as catalysts in the ammonia plant. The following statistical indices i.e., Pearson correlation matrix, geo-accumulation index (Igeo), contamination factor (Cf), degree of contamination (Cd), pollution load index (PLI) and ecological risk potential (RI) factors were taken into account to assess the heavy metals contamination of the sediments. According to the values of the statistical indices for Cr, Mn, Ni, Cu and Zn, it is concluded that the study area was with low contamination while concentrations of Ni and Cu were higher than the Threshold Effect Level (TEL) and Toxicity Reference Value (TRV) values suggesting unsafe to use the sediments for vegetation and other uses.