Bacterial taxa of potential public-health relevance and predicted antimicrobial-resistance functions are important in effluent management. This study compared bacterial communities, environmental associations, and predicted functions in aquaculture effluents (Group A) and wastewater treatment plant effluents (Group W) from the Mi River Basin, China, using a 16S rRNA-based framework, with the WHO 2024 Bacterial Priority Pathogens List used for contextual interpretation. relatively consistent profiles, with Acinetobacter, Limnohabitans, and Pseudomonas among abundant genera. Group W showed site-specific patterns, including high relative abundances of Legionella, Flavobacterium, and Mycobacterium in W3 and Pseudarcobacter and Arcobacter in W4 and W5. Among 400 genus–factor correlations, only the negative Sphingorhabdus–COD association remained significant after BH correction. The aggregate predicted abundance of six ARG-related KOs was 2.22-fold higher in Group A. The tetA-type KO was higher in Group A, whereas erm-type was higher in Group W. Seven samples had abundance-weighted NSTI values below 0.10, and directional patterns remained after excluding W5. Although 16S-based analyses cannot directly confirm pathogens or ARGs, the framework distinguished effluent-specific microbial and predicted resistance-related patterns, supporting large-scale routine monitoring and tiered risk management for water reuse and receiving waters.