<p>This study examines the impact of plant extracts from traditional Chinese medicinal herbs on water quality, microbial communities, and pathogen dynamics in pond-based aquaculture systems. Conducted over 40 days at an ecological aquaculture farm in Jinshan District, Shanghai, the experiment involved six ponds—three serving as controls and three as treatment groups, each stocked with 1000 crucian carps (<i>Carassius auratus</i>). Regular applications of plant extracts and water sampling every ten days were performed. Results showed significant enhancements in water quality parameters, including increased pH, dissolved oxygen, and ammonia nitrogen, alongside reductions in total nitrogen, nitrite nitrogen, and chlorophyll a. Microbial diversity analysis indicated a shift towards beneficial taxa, such as Planctomycetota and Bacillariophyta, correlating with improved water quality. Notably, the abundance of opportunistic pathogens, including <i>Streptococcus suis</i>, decreased significantly, suggesting a healthier aquatic environment. Analysis of the intestinal microbiota in cultured crucian carp also revealed a reduction in pathogenic species, including <i>Streptococcus suis</i> and <i>Aeromonas hydrophila</i>. These findings underscore the potential of plant extracts to enhance aquaculture health by optimizing water quality and promoting microbial balance, thereby mitigating pathogen risks.</p> Graphical Abstract <p></p>