Trace metal contamination of water and sediment may have a serious ecological risk to aquatic environmental health. The present study was organized to determine the five globally alarming heavy metals (Cu, Zn, Pb, Cd and Cr) levels in the sediment and assess their potential biological danger. Five different stations were chosen to collect the sediment samples of Meghna River Estuary during two different seasons; monsoon and post monsoon. Results demonstrated the descending order of the observed metals in sediment as follows: Zn< Cr < Cu < Pb < Cd.  Geo-accumulation index (Igeo), CF (contamination factor), PLI (Pollution Load Index) and PERI (Potential ecological risk index) were calculated to evaluate contamination level which suggested that Meghna River Estuary is not contaminated with those metals and there is no risk of ecological degradation. Furthermore, the multivariate analysis, such as PCA and Pearson correlation matrix analysis disclosed that Zn and Pb may have originated from anthropogenic sources, and other metals may come primarily from a natural source.