Abstract: Sustainable aquaculture has gained much attention in recent years. It is still lacking in the ecological dynamics of the microbial communities in the pond-rice field recirculating systems. The integrated systems can combine aquaculture with the constructed wetlands in the nutrient cycling and water quality. However, only a little is known about the succession of the microbial communities, their interaction patterns, and the process shaping their assembly over time and space. In this study, a systematic investigation was carried out to explore the spatiotemporal variation in the planktonic bacterial communities in such systems. An attempt was also made on their responses to environmental changes and the relative contributions of the deterministic and stochastic factors in the community assembly. A representative rice–fish co-culture system was selected as the experimental model. The recirculating water flow was divided into three functional zones: the inlet section (receiving nutrient-rich pond effluent), the field section (a rice paddy wetland functioning as a biofilter), and the outlet section (a discharge area with reduced nutrient concentrations). Two fixed sampling sites were established in each zone. The water samples were collected monthly in the peak period of the rice cultivation and fish farming from April to August 2022. Temporal dynamics were captured after sampling. High-throughput sequencing targeting the 16S rRNA gene was employed to identify the bacterial taxa. The community composition, richness, and evenness were assessed after comprehensive bioinformatic and statistical analysis. Furthermore, the alpha and beta diversity indices, principal coordinate analysis (PCoA) with Bray–Curtis dissimilarity, and canonical correspondence analysis (CCA) were utilized to explore the relationships between bacterial communities and environmental variables. In addition, the bacterial co-occurrence networks were constructed to examine the microbial interaction patterns. Ecological assembly was then inferred using both neutral community models and niche-based frameworks. The relative influence of the stochastic and deterministic factors was evaluated to shape the bacterial community structure. The results indicated that the rice field and constructed wetland played a crucial role in the nutrient removal and water quality. The average removal rates of the total phosphorus (TP), total nitrogen (TN), ammonia nitrogen (NH₃-N), nitrate nitrogen (NO₃⁻-N), and nitrite nitrogen (NO₂⁻-N) were 65.5%, 47.3%, 51.2%, 56.4%, and 53.3%, respectively, indicating the strong purification of the system. Temporally, there was a significantly seasonal variation in the composition of the bacterial community (P<0.05), particularly in response to the environmental gradients, such as the temperature and nutrient concentrations. Spatially, the overall structure of the bacterial community remained relatively consistent across the three sections; However, the bacterial taxa shared the localized changes in the relative abundance and community evenness. Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla in most samples. Co-occurrence network analysis revealed that the field section also exhibited the most complex network of the bacterial interaction, indicating the high modularity, centrality, and clustering coefficients. There was the strong environmental filtering and pronounced ecological niche differentiation in the rice wetland. The environmental variables, NH₃-N, NO₃⁻-N, and NO₂⁻-N were measured to identify them as the key driving factors on the bacterial community shifts. Moreover, the ecological modeling showed a gradual increase in the contribution of the stochastic factors along the direction of water flow. There was a shift from the predominantly deterministic assembly near the inlet to the more random community assembly downstream. The environmental filtering intensity was reduced to increase the microbial dispersal or ecological drift. In conclusion, this finding can provide a comprehensive overview of the spatiotemporal patterns and ecological assembly of the bacterial communities in an integrated rice-fish farming system. The theoretical insights can be offered to understand the influence of the environmental factors on the bacterial community structure in the recirculating agricultural wetlands. As such, the microbial community can also be optimized to support the ecological design and management of the integrated rice-fish farming systems.