Contamination of heavy metals in sediment is regarded as a major crisis globally, with a large SHARE in developing countries, such as Bangladesh. The objective of this study is to assess the contamination level and seasonal variation of heavy metals and their ecological risk in sediments. Heavy metals (Cr, Ni, Cu, As, Cd, and Pb) in sediments were investigated from eight different sites of Paira River situated at the southern part of Bangladesh and metals were measured by using inductively coupled plasma mass spectrometer. The mean concentration of Cr, Ni, Cu, As, Cd, and Pb in sediments was 45, 34, 30, 12, 0.72 and 25 mg/kg dw, respectively. Metals in sediment during winter were higher than summer season. The concentrations of metals in sediment were compared with both background and toxicological reference values. The comparative results suggested that the selected metals created an adverse effect on the aquatic ecosystems of the studied river. The pollution load index for three sites were higher than baseline values indicating progressive deterioration of sediments by heavy metal. Potential ecological risks of metals in sediment indicated moderate to considerable risk. This study suggested that more attention should be directed to the comprehensive risk assessment of heavy metals of this riverine aquatic environment.