This study examined microbial community dynamics across water, soil, and intestinal samples in Litopenaeus vannamei aquaculture ponds over 8 weeks. Sample type was the primary driver of community structure (P < 0.001), with soil exhibiting highest diversity (observed richness: 2,671 ASVs, Shannon: 6.76, Faith’s PD: 282.36), followed by intestine (observed richness: 891 ASVs, Shannon: 4.54, Faith’s PD: 117.77) and water (observed richness: 512 ASVs, Shannon: 3.58, Faith’s PD: 89.25). Soil showed highest evenness (Berger-Parker: 0.05), while water exhibited strongest dominance (0.23). Significant interactions for sample type and interaction for observed richness and Faith’s PD (P < 0.018 and P = 0.006) revealed that intestinal samples increased from 597 to 1,237 ASVs, indicating active colonization, while soil and water remained relatively stable. At the genus level, soil demonstrated highest temporal stability (746 genera, 48.57%), followed by intestine (422 genera, 31.8%) and water (130 genera, 13.32%). Soil-intestine sharing intensified from 25.04% to 33.11%, demonstrating progressive soil-mediated gut colonization. Core shared genera across all sample types ranged from 14.2-22.95%, peaking at Weeks 2-4, while water showed minimal uniqueness (1.84-2.73%). Compositionally, Vibrio spp. emerged as the dominant intestinal genus (10-20%, Weeks 2-6), demonstrating host-specific colonization patterns, while soil remained stable with low abundance taxa dominating (50-60%) and water showed dramatic shifts with G7-14 increasing to 40% by Week 8. Differential abundance analysis confirmed strong intestinal enrichment for Vibrio spp. (log fold change 6-9), indicating host-specific colonization, while soil harbored the greatest diversity of habitat-specific taxa.