Coastal microbial communities integrate anthropogenic chemical pressure across time and space, but their utility as candidate pollution indicators depends on resolving where in the ecosystem the pollution-associated microbial signal is strongest. In this study, we determined the taxonomic diversity of bacterial and archaeal communities in two contrasting subtropical embayments in Hong Kong, the heavily impacted, Pearl River Estuary-influenced Deep Bay and the less anthropogenically influenced Ko Lau Wan, allowing an embayment-scale comparison between coastal systems with contrasting anthropogenic pressure in the northern South China Sea. Sampling spanned three microhabitats (free-living, particle-attached, and sediment) and four seasons. Community composition was structured primarily by microhabitat, which explained 40.6% of compositional variation and clearly separated water-column fractions from sediments. The embayment-level association was persistent over seasons: 23 of 24 indicator taxa retained the same embayment association across all four seasons, indicating a consistent pattern associated with anthropogenic pressure rather than seasonal noise. Multivariate models controlling for spatial and seasonal structure identified nutrients, trace metals, and pharmaceuticals as primary chemical correlates of community composition. PFAS emerged as a robust year-round predictor of community composition after accounting for spatial and seasonal structure (partial R² = 11.5%), while short-chain chlorinated paraffins (SCCPs) showed particularly strong associations with sediment communities. Predicted functional profiles (PICRUSt2) reinforced these patterns: metal-stress, pollutant-degradation, and antibiotic-resistance pathways co-varied with measured contaminants, with sediment antibiotic-resistance pathways most strongly correlated with SCCPs (Spearman ρ = 0.54). Microhabitat-resolved microbial and predicted functional signatures track diverse anthropogenic contaminants, including PFAS and chlorinated paraffins of direct regulatory concern in China, and could serve as cost-effective, integrative candidate indicators for multi-contaminant coastal monitoring in Hong Kong coastal waters and comparable subtropical systems.