Background: In rural China, many natural water bodies and farmlands have been converted into fish farming ponds as an economic developmental strategy. There is still a limited understanding of how the diversity and structure of microbial communities change in nature and become managed fish pond ecosystems.

Objective: We aimed to identify the changes of the diversity and structure of microbial community and driving mechanism in pond ecosystems.

Methods: The datasets of 16S rRNA amplicon sequencing and the concentrations of N and P fractions were achieved in water samples of pond ecosystems. Bioinformatics analysis was used to analyze the diversity and structure of the microbial communities.

Results: Our results indicated that the diversity and structure of the microbial communities in the natural ponds were significantly different from ones in managed fish ponds. The nutrients of N and P and water environmental factors were responsible for 46.3% and 19.5% of the changes in the structure and diversity of the microbial community, respectively.

Conclusion: The N and P fractions and water environmental factors influenced the microbial community structure and diversity in pond ecosystems. Fish farming indirectly affected the microbial community by altering the contents of N and P fractions in water bodies of ponds, when a natural pond was converted into a managed fish pond.