Bacterial populations in intensive striped catfish (Pangasianodon hypophthalmus) ponds remain poorly understood. This study aimed to unravel the bacterial community structure in water and bottom sediment in catfish ponds during the rainy season, using next-generation sequencing technology. Next-generation sequencing data showed 23 phyla, 40 classes, 92 orders, 133 families and 242 genera in striped catfish ponds. 32 genera were common to both water and sediment, while 168 genera were confined to pond water and 42 genera were confined to bottom sediments. Pond water had higher biodiversity and harboured more genera than sediment. Proteobacteria, Fusobacteriota and Actinobacteriota were the most dominant phyla in water, while the four most dominant phyla in the sediment sample were Actinobacteriota, Myxococcota, Desulfobacterota and Proteobacteria. Novosphingobium was the most abundant genus in the water, while Nitrospira was the most abundant in sediment. In addition, the pathogenic bacteria Aeromonas, Flavobacterium, Edwardsiella and Bacillus, a common probiotic, were also detected in water and sediment, but with much lower abundances than Novosphingobium and Nitrospira.