As global food security issues become increasingly severe, an important innovation in agricultural production patterns, namely integrated rice–fish farming, has been widely implemented around the world, especially in Asia. To assess the impact of integrated rice–crayfish (Procambarus clarkii) farming (IRCF) on agricultural ecosystems, we used Illumina high-throughput 16S rRNA gene sequencing to analyze differences in diversity, composition, co-occurrence network, and assembly process of planktonic bacterial communities in paddy water between traditional rice farming (TRM) and IRCF. Environmental factors and planktonic bacterial communities were evaluated during the tillering, jointing, flowering, and grain-filling stages on August 24, September 5, September 24, and October 16, respectively. Our findings revealed that, throughout the entire cultivation period, IRCF had no notable impacts on bacterioplankton community diversity in paddy water, but it changed the composition and relative abundance of the dominant bacterioplankton. Specifically, IRCF promoted the Chloroflexota during the tillering stage but reduced its presence during the grain-filling stage. It also significantly decreased the Bacillota during the jointing stage while notably enhancing Actinomycetota during the flowering stage. Furthermore, IRCF markedly improved the robustness and negative/positive cohesion within bacterioplankton co-occurrence networks during jointing and grain-filling stages. IRCF altered the assembly processes shaping planktonic bacterial communities, promoting a greater dominance of stochastic processes during the tillering, jointing, and flowering stages and a diminished dominance during the grain-filling stage. IRCF dramatically changed aquatic environmental factors, particularly during the jointing stage, by substantially increasing the TN, ammonium, nitrate, and phosphate levels in paddy water. These nutrient levels were closely correlated with the dynamics of the planktonic bacterial communities. Our findings underscore the considerable potential of IRCF in enhancing the stability of bacterioplankton communities and promoting rice growth while also providing valuable data and theoretical insights into the microbiological ecological impacts of IRCF on the agroecosystem.
