The study was conducted to investigate the relationship between zooplankton composition and water quality in Bac Vam Nao flood control area, An Giang. Three samples of plankton and water quality (S1, S2, and S3) were collected in March and September 2020. The results showed that the water quality in the study area was contaminated with organic matters, nutrients and coliform, in which the water quality in the dry season was more polluted than that in the rainy season. Through two monitoring of the zooplankton in the Bac Vam Nao flood control area in 2020, 35 species belonging to four phyla Amoebozoa, Rotifera, Arthropoda and Larva were detected. The Rotifera phylum had the richest species composition with 22 species (accounting for 62.9%) while the lowest was the Larva division with one species recorded (accounting for 2.9%). The Shannon-Weiner biodiversity index (H') ranged from 1.64 to 2.12 corresponding to water quality ranged from slightly polluted to polluted. The WQI (32-62) showed the water quality from moderate pollution to poor. It was found that H' and WQI were different in water quality indicating. The difference could be because zooplankton is additionally influenced by other factors such as food sources and predators. Therefore, water quality indication using zooplankton index should be used with expertise.