[Background] Aquaculture diseases are a significant constraint in the development of freshwater fisheries, and the microbial status of aquaculture environment is closely related to the health of fishes, which has drawn extensive attention. [Objective] To elucidate the change characteristics of pathogen abundances and bacterial community diversity in aquaculture environment. [Methods] real-time fluorescence quantitative PCR method and terminal restriction fragment length polymorphism (T-RFLP) technology were used to quantify typical pathogens in gibel carp breeding environment, and to analyze bacterial community diversity. [Results] Pathogen abundances in the process of breeding presented different change trend, the abundances of Aeromonas hydrophila, A. sobria and A. veronii were significantly positively related to Cyprinid herpesvirus Ⅱ. The abundance of pathogens in water was significantly affected by pH, temperature, dissolved oxygen and other environmental factors. T-RFLP analysis showed that the composition of bacterial community in sediment samples was more complex than that in water samples, and the dynamic change range of bacterial community in sediment was higher than that in water. The T-RFs in water and sediment ranged from 11 to 29 and 20 to 32, respectively, and Shannon-wiener index ranged from 1.44 to 2.87 and 2.44 to 3.25, respectively. [Conclusion] The abundances of pathogens in cultured waters were higher than that in sediments, and the relative abundance and diversity of bacterial community in sediments were higher than that in water. The changes of pathogen abundances and bacterial community structure are closely related to environmental factors, and it will provide theoretical data for guiding the early warning of pathogenic diseases in the breeding processes to clarify the ecological distribution and abundance changes of pathogenic microorganisms in the aquaculture pond.