Industrialized aquaculture of seafood is the main global protein supply. But tail water discharge is the source of pollution in coastal waters, which the reuse research is insufficient. Therefore, in this study, in-situ sampling and high-throughput detection were used to analyze the sediment in the Yongfeng River and the drainage canal in Yellow River Delta, exploring the potential in-situ biological technique. The results showed that the dominant bacteria in the upper reaches of Yongfeng River were consistent with those in the discharge area, mainly Gillisia (25.44%-60.35%) and Psychrobacter (4.26%-7.36%). Meanwhile Psychrobacter (23.27%-56.73%) and Proteiniclasticum (16.24%-39.58%) were the main components in the sediments of the downstream and the estuary. Principal Coordinate Analysis (PCoA) revealed some differences in bacterial communities between the Yongfeng River and the drainage channel sediment. And metabolic analysis indicated that a considerable amount of organic matter in the drainage channel was affected by aquaculture tailwater, leading to an increase in specific degradation. It was found that maintaining osmolality might be crucial for the growth of bacteria in costal sediment. In terms of archaea, the upstream sediments were mainly Candidatus Nitrocosmicus (7.14%-22.98%) and Methanosaeta (13.08%-25.69%), while the main in pollution sources were Marine Group II (39.38%). Nitrososphaeraceae (32.70%-78.17%) and Methanogenium (2.19%-11.24%) were the dominant species in the downstream and estuary sediments. Through PCoA analysis, it was found that there is some similarity in the archaeal communities between the samples. Metabolic analysis revealed that archaea has better adapted to seawater osmotic pressure. Archaea are also more susceptible to organic matter input, which the archaea may participate in the terminal degradation process of aromatic metabolism. The results reveal that the aquaculture effluent has a high potential for methanogens, but its diverse organic carbon requires a variety of degrading bacteria to participate in improving efficiency. [Chinese Fishery Quality and Standards, 2023, 13(6): 11-18]