INTRODUCTION: Bacterial communities play crucial roles in the functioning and resilience of aquatic ecosystems, and their responses to water pollution may be assessed from ecological niches. However, our understanding of such response patterns and the underlying ecological mechanisms remains limited. METHODS: In this study, we comprehensively investigated the effects of water pollution on the bacterial structure and assembly within different ecological niches, including water, sediment, submerged plant leaf surfaces, and leaf surfaces, using a 16S high-throughput sequencing approach. RESULTS: Ecological niches had a greater impact on bacterial community diversity than pollution, with a distinct enrichment of unique dominant phyla in different niches. This disparity in diversity extends to the bacterial responses to water pollution, with a general reduction in α-diversity observed in the niches, excluding leaf surfaces. Additionally, the distinct changes in bacterial composition in response to pollution should be correlated with their predicted functions, given the enrichment of functions related to biogeochemical cycling in plant surface niches. Moreover, our study revealed diverse interaction patterns among bacterial communities in different niches, characterized by relatively simply associations in sediments and intricate or interconnected networks in water and plant surfaces. Furthermore, stochastic processes dominated bacterial community assembly in the water column, whereas selective screening of roots and pollution events increased the impact of deterministic processes. DISCUSSION: Overall, our study emphasizes the importance of ecological niches in shaping bacterial responses to water pollution. These findings improve our understanding of the complicated microbial response patterns to water pollution and have ecological implications for aquatic ecosystem health.