The study was conducted to assess biodiversity and water quality using the Shannon-Wiener biodiversity index (H') in the Bac Vam Nao flood control area, An Giang province in 2020. The finding shows that the composition of phytoplankton in the rainy season is more diverse than that in the dry season. The results of analysis of phytoplankton samples at three locations in the Bac Vam Nao flood control area recorded 71 species belonging to 5 different algae phyla, including Cyanophyta, Bacillariophyta, Chlorophyta, Charophyta and Euglenophyta. In which, Euglenophyta has the richest species composition with 25 species (accounted 35.2%) and the lowest is the Cyanophyta with 05 species (7%). The dominant species through two monitoring periods are those of the Bacillariophyta (Cyclotella meneghiniana, Melosira granulata) and Cyanophyta (Oscillatoria sp.). At the monitoring positions of the Bac Vam Nao flood control area, one toxic algae species and two harmful algae species were detected out of a total of 04 species of blue-green algae. The Shannon-Wiener (H') diversity index ranges from 0.56 to 4.18, the H' index in the dry season is higher than that in the rainy season. Surface water quality in Bac Vam Nao flood control area according to diversity index H' is classified from very polluted to clean. It is necessary to expand the scope of research areas to better understand the role of phytoplankton as a water quality indicator, serving effective water quality monitoring, reducing costs and environmental pollution due to the use of chemicals during water sample analysis.