It is increasingly recognized that Estuarine Set Bag Net (ESBN) is very popular gear in the coastal fishing community of Bangladesh. In order to reveal the species composition of the ESBN catch and to study the impact of environmental parameters on the spatio-temporal variation of fish assemblages, a one-year baseline survey was conducted in coastal waters of the Moheshkhali Island, northern Bay of Bengal, Bangladesh. A total of 59 taxa were identified of which 47 were finfishes, 7 were shrimps and 5 were from other categories i.e. crab, holothruim, lobster, squid and squila. Among them, 54 species were commonly distributed in all four seasons and stations with 23 and 24 species were found dominant to the total communities in different seasons and sites, respectively. Similarity percentage analysis revealed significant variation in structure and composition of total communities in temporal and spatial scale: (1) the highest (89.33%) and lowest (70.10%) average species similarity was observed in monsoon and winter, respectively; (2) the average species similarity was found highest in Sonadia (88.30%) and lowest in Nalbila (74.83%). SIMPER analysis demonstrated that the contributory species (i.e. Crab, Squid, Pampus chinensis, Chirocentrus nudus, Ascetes sp. Penaeus monodon, Metapenaeus brevicornes, Arius sp., Tenualosa ilisha, Uranoscopus sp., Machrobrachium ruddis, Gerres filamentosus, Coillia dussumieri, Squila, Glossogobius giuris, Rastrelliger kanagurta, Rhynchorhamphus georgii, Chirocentrus nudus, Ascetes sp., Metapenaeus brevicornes, Tenualosa ilisha, Uranoscopus sp., Rhynchorhamphus georgii, Penaeus indicus) varied among different sites and seasons. One-way ANOVA and Canonical Correspondence Analysis (CCA) revealed that the total communities were significantly driven by temperature, salinity, pH, DO and water transparency. Multivariate analyses showed that the diversity of ESBN fishery is high in this Island. These findings signify that this coastal zone is one of the nursery grounds and highly diversified for many marine fishes.