The aquaponics system, an integrated ecological agriculture model, effectively combines aquaculture and the cultivation of aquatic plants. This system not only utilizes the nutrients in aquaculture water to promote plant growth but also purifies water quality through plant absorption, reduces the discharge of aquaculture waste, and provides novel ideas for the green transformation of the aquaculture industry. Microorganisms are crucial in the aquaponics system for elemental cycling, water quality purification, ecological balance maintenance, and healthy growth regulation of flora and fauna. The co-occurrence of bacterial and microeukaryotic species in aquaculture water is a common ecological phenomenon; however, research on the interactions between bacterial and microeukaryotic communities remains relatively limited. Currently, insufficient research exists on the complexity and structural characteristics of microbial community diversity in aquaculture waters of aquaponic systems, and the interactive relationship between bacteria and microeukaryotic communities remains unclear, thereby limiting the optimization and regulation of system operations via microbial methods. In this study, we constructed an aquaponic system as the experimental group and a recirculating water system as the control group. We conducted a 78-day aquaculture experiment, collected water samples from aquaculture ponds,and employed high-throughput sequencing technology targeting the 16S rRNA and 18S rRNA genes to assess the diversity and structural composition of microbial communities in aquaculture waters from different treatment systems. We also revealed the differences in microbial community composition, bacterial networks, microeukaryotic networks, and bacterial-microeukaryotic interaction network structures between different systems, with the objectives of clarifying the differences in bacterial and microeukaryotic community diversity, structure, and composition between the aquaponic and recirculating water aquaculture systems and understanding the structural differences in the microbial community co-occurrence networks between systems. This provided a theoretical basis for establishing aquaponic systems from a microbial mechanism perspective. The observed species, Chao1, and Pdfaith indices of the bacterial community in the control group were significantly higher than those in the aquaponic group (P＜0.05), and a significant difference was observed in the microeukaryotic community structure (ANOSIM R = 0.082, P= 0.036). Significant differences were noted in the diversity of the bacterial communities and the structure of the microeukaryotic communities among the different treatment groups. At the phylum level, Bacteroidota and Fusobacteriota exhibited increased relative abundances in the aquaponic group, whereas the relative abundance of Chlorophyta was lower than that in the control group. The relative abundance of Chlorophyta in the aquaponic group continuously decreased over time, whereas it consistently increased in the recirculating aquaculture group. At the genus level, Flavobacterium, Cetobacterium, and Anurofeca were more abundant in the aquaponics group than in the control group. Significant differences were observed between the aquaponic and control groups in the compositions and relative abundances of the dominant bacterial and microeukaryotic groups. Analysis of the microbial community co-occurrence network showed that the bacterial and microeukaryotic communities in the aquaponic group had more complex interactions and network structures than those in the control group, with more pronounced competitive relationships and greater stability among microbial communities. Additionally, the network structures of the microeukaryotic communities in both the aquaponic and control groups were more complex than those of the bacterial communities, with more intense internal competition and greater stability. Bacterial-microeukaryotic interaction network analysis indicated that, in the aquaponic group, Bacteroidota and Chlorophyta were the core nodes of the bacterial-microeukaryotic interaction network. In the control group, Proteobacteria and Fusobacteriota were the core nodes of the bacterial-microeukaryotic interaction network. Substantial differences existed in the interaction relationships between bacterial and microeukaryotic communities and the proportions of various groups between the aquaponic and control groups. The interaction relationships between bacterial and microeukaryotic communities in the control group were more complex and closer than those in the aquaponic group, which exhibited more antagonistic relationships. This study analyzed the differences in diversity, compositional structure, and co-occurrence networks of bacterial and microeukaryotic communities between aquaponic and recirculating water aquaculture systems. The growth performance, immunity, and digestive function of fish in the aquaponic system were significantly better than those in the recirculating water aquaculture system, highlighting the advantages of aquaponic systems. This study elucidated the microbial community characteristics of aquaponic and recirculating water aquaculture systems and revealed the interactive relationships between bacterial and microeukaryotic communities in both aquaculture modalities to provide a theoretical microbial basis for the stable operation of aquaponic systems.