1401-1409In this study, the assemblage structure of nektonic fauna were studied in relation to some important environmental variables in the Meghna Estuary, the largest estuarine ecosystem of Bangladesh. Silica, nitrite, phosphate, and total suspended solids (TSS) were found to be positively correlated with fish species abundance. Nitrite and TSS showed significant difference, and water pH, salinity, transparency, water temperature, and dissolved oxygen were found to be negatively correlated. The results of similarity analysis showed a significant difference between different sampling stations and seasons, and revealed that finfish species like Trypauchen vagina, Polynemus paradiseus, Johnius dussumieri, Harpodon nehereus contributed significantly (>10.0%) to the fish abundance structure of each sampling station. Cluster analysis shows 53% similarity level in the abundance of fish in different seasons and sampling stations. Significant effect of water transparency and salinity was observed through Canonical Correspondence Analysis (CCA) in shaping assemblage structure and species distribution