Bioremediation technology has been widely recognized as a sustainable treatment method for purifying aquaculture wastewater. We established two types of ecological floating beds, one with water spinach (WS) only and another with water spinach combined with exogenous compound bacteria (WS-ECB) for the treatment of the Pacific white shrimp aquaculture wastewater of low-salinity. The exogenous compound bacteria used in this study was composed of Rhodopseudomonas palustris and Bacillus subtilis in a certain proportion. Microbial community dynamics were analyzed by using high-throughput sequencing of 16S rRNA and water quality was determined. Both two treatments were effective in the remediation of aquaculture wastewater. The removal efficiencies of CODMn, TN and TP in the WS group were 34.33 %, 66.54 % and 73.01 %, respectively, and the removal efficiency of NH4+ in the WS-ECB group was 93.79 %. Furthermore, the addition of water spinach and exogenous compound bacteria increased the abundance of some bacteria that are involved in regulating water quality and altered the succession of microbial communities. The microbial communities were shaped by both stochastic processes (including limited dispersal) and deterministic processes (including environmental conditions and biotic interactions). Importantly, stochastic processes dominated the assembly of both water and rhizosphere microbial communities in different treatments, while deterministic processes contributed more to the rhizosphere microbial community in the WS-ECB than in the WS. Overall, our study emphasizes that plant and microbial remediation was a potential and effective approach to remove the nutrients of water, and clarifies the bacterial community dynamics and assembly mechanisms during aquaculture wastewater treatment processes.