An increasing number of investigations have shown the universal existence of arbuscular mycorrhizal fungi (AMF) in aquatic ecosystems. However, little is known about the accurate distribution and function of AMF inhabiting aquatic ecosystems, especially ecological floating beds (EFBs), which are constructed for the remediation of polluted water bodies. In this study, we collected root samples of Canna generalis, Cyperus alternifolius, and Eichhornia crassipes from three EFBs on two eutrophic lakes in Wuhan, China. We aimed to investigate the resources and distribution of AMF in EFBs using Illumina Mi-seq technology. A total of 229 operational taxonomic units (OTUs) and 21 taxa from 348,799 Glomeromycota sequences were detected. Glomus and Acaulospora were the most dominant and second most dominant genera of AMF in the three EFBs, respectively. Different aquatic plant species showed varying degrees of AMF colonization (3.83-71%), diversity (6-103 OTUs, 3-15 virtual taxa), and abundance (14-57,551 sequences). Low AMF abundance, but relatively high AMF diversity, was found in C. alternifolius, which is usually considered non-mycorrhizal. This finding indicated the high accuracy of Illumina sequencing. Our results also revealed a lognormal species abundance distribution that was observed across AMF taxa in the three plant species. The AMF community composition was closely related to nitrogen and phosphorus contents. Overall, our data show that EFBs harbor diverse and abundant AMF communities. Additionally, the AMF community composition is closely related to the water quality of eutrophic lakes treated by the EFBs, indicating the potential application of AMF in plant-based bioremediation of wastewater. Keypoints center dot Aquatic plants in EFBs harbor diverse (229 OTUs) and abundant (348,799 sequences) AMF. center dot Different plant species host different taxa of AMF. Cyperaceae, originally considered non-mycorrhizal, may in fact be a variable mycorrhizal plant family. center dot The AMF community composition in EFBs is closely related to nutrient concentrations (nitrogen and phosphorus).