In recent years, the number of small greenhouse farms in China has expanded rapidly. Within the aquaculture process of these small greenhouses, microorganisms play a key role in decomposing residual bait and feces in the water column. However, the lack of nutrient-degrading microbial taxa in the water column, combined with excessive baiting by farmers, often leads to the accumulation of inorganic nitrogen. This accumulation negatively affects the yield and economic benefits of cultured species. The present study was conducted to investigate the differences in water quality, as well as the structure and function of particle-associated bacteria (PAB) and non-mobile free-living bacteria (NFB) in small greenhouse farms. This investigation focuses on the turbidity of the water column caused by the increasing concentration of suspended particles during the aquaculture process, in order to reveal the factors influencing the culture yield. Differences in the structure and potential function of the two bacteria were analyzed by high-throughput sequencing of 16S rRNA. Additionally, real-time fluorescence quantitative PCR was used to detect the abundances of ammonia-oxidizing bacteria amoA and nitrite-oxidizing bacteria nxrB, both of which are associated with nitrogen transformation in suspended particles. The results of this study showed that the concentration of suspended particles was significantly higher in high-yield small greenhouses compared to low-yield small greenhouses (P＜0.001). Additionally, the concentration of suspended particles in the water column was closely related to shrimp production. The Chao1 and Shannon indices of PAB were found to be higher than those of NFB in the aquaculture water column of small greenhouses, indicating greater diversity and abundance of PAB. Notably, Flavobacteriaceae were significantly enriched in PAB, indicating that they were the dominant functional microorganisms in PAB. The abundance of biosynthesis, material, and energy metabolism functional pathways in PAB was significantly higher than that in NFB (P＜0.05). Among these ways, nitrification-denitrification was notably upregulated in PAB, indicating that PAB is more capable of material synthesis and nutrient metabolism. Real-time fluorescence quantitative PCR results revealed that the abundances of major functional genes of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were higher in the PAB of high-yield small greenhouses than in those of low-yield small greenhouses, indicating that nitrifying bacteria were more mature in the PAB of high-yield small greenhouses. This study demonstrated that PAB play an essential role in the removal of nitrogenous pollutants from aquaculture water in small greenhouse farms, which further affects shrimp production by regulating water quality. The results of this study provide an important theoretical basis for water quality control and efficient shrimp culture in small greenhouse farms.