Phu My species-habitat conservation area (PMCA) is a seasonal wetland area; thus, water quality plays an essential role in the development of organisms. Therefore, the study was carried out to assess surface water quality based on phytoplankton, zooplankton and benthic composition at PMCA, which has been little studied. The phytoplankton, zooplankton and benthic samples were collected at six locations (N1-N6) of the habitats and canals in November 2021. Shannon-Wiener biodiversity index (H’), Pielou index (J) and average score per taxon (ASPT) were used to assess pollution levels of surface water. A total of 71 species of phytoplankton belonging to fve phyla (i.e., Chlorophyta, Euglenophyta, Bacillariophyta, Dinophyta and Chrysophyta), 57 species of zooplankton belonging to three phyla (i.e., Protozoa, Rotifera, Arthropoda) and two benthic species belong to two groups (i.e., Oligochaeta and Insecta) were detected. The phyla of Euglenophyta, Rotifera, and Insecta were the dominant groups in species composition and the phyla of Chlorophyta, Protozoa, and Insecta were dominated in terms of individual density. Species of Trachelomonas volvocina, Phacus torta, Euglena oxyuris, Arcella vulgaris, Brachionus bidentata, Lecane hastata, Lecane bulla, Lecance pyriformis and Polyarhtra vulgariis appeared at most of the studied sites, indicating the organic and nutrient pollution of the water bodies. The Shannon-Wiener biodiversity index (H’) and Pielou index (J) showed the water quality from moderate to severe pollution. The results of water quality classifcation according to ASPT and H’ of benthic animals had similar characteristics, indicating that the surface water is very dirty (heavy pollution). The current fndings could be used to manage water quality in the future to conserve biodiversity. Furthermore, it helps to improve and expand methods for monitoring surface water quality in the conservation area, in addition to evaluating based on physical and chemical parameters.