The Payra River is one of the large coastal rivers in Bangladesh which supports incredible fish species and has been affected by extensive human disturbance due to huge fishing pressure. The present study provides information about the temporal diversity of finfish and shellfish concerning climatological variables and ecological pollution along with threat assessment in the Payra River, Patuakhali. During the entire study, a total of 61 fish species including 56 finfish and 5 shellfish species were recorded under 22 families belonging to 11 orders. The order-wise fish species availability showed that the Perciformes (29.49%) was the dominant order based on species richness. Among them, 4 endangered, 6 vulnerable, 4 near threatened, 42 least concern, and 5 data deficient species were found. During the study period, the average Shannon-Weaver diversity index value was (3.33±0.12) indicates a good spread of fish population in the Payra river. Average Margalef richness index value was found (7.60±0.32), Pielou's evenness index (0.48±0.05), and Simpson dominance index (0.93±0.02) in Payra river. Dominance and Richness index value indicates clear water environment to slight pollution in the Payra river. Ten different kinds of fishing gears were identified under 3 major groups including 5 nets, 3 hooks and lines, and 2 traps. The phytoplanktonic genus and species revealed moderate pollution. Canonical correspondence analysis ordination plot showed that rainfall was the most influencing driving force among the meteorological parameters. The cluster analysis based on the Bray-Curtis similarity matrix showed that the winter season formed a separate cluster. In the recapitulation, the Payra River is a highly productive system that provides a favorable environment for a large variety of finfish and shellfish species assemblages. Findings of the conducted study are expected to be helpful for the respective researchers, policymakers, managers, and conservationists for the sustainable management of this water body and the interconnected surrounding neighboring countries.