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Shrimp aquaculture ponds are dynamic ecosystems in which water quality and microbial interactions play a central role in animal health. This study aimed to investigate the relationship between the intestinal microbiota of Penaeus monodon and the microbial community of mixed-culture pond water. Water quality indicators showed progressive changes from July to September, with pH decreasing from 8.1 to 7.5 but remaining within a suitable range. Nitrogen compounds, including ammonia, nitrite, and nitrate, increased steadily, with total nitrogen rising from 0.71 to 1.86 mg·L⁻¹, while phosphate and total phosphorus reached 0.31 and 0.36 mg·L⁻¹, respectively, exceeding thresholds commonly associated with algal bloom risk. Microbial community profiling using Illumina MiSeq sequencing revealed 166 OTUs shared between shrimp intestine and pond water, while both habitats contained more than 350 OTUs overall. Alpha diversity analysis showed higher microbial richness in water than in shrimp intestines, dominated by unclassified taxa, whereas shrimp guts were enriched in specific genera such as Vibrio. Cluster analysis indicated partial overlap but distinct grouping of gut and water microbiota, with the PMB intestinal community diverging most strongly. These findings highlight a close link between water quality and microbial composition, emphasizing the importance of pond management for maintaining ecological stability and shrimp health.