The study was conducted in March 2019 in three areas subject to impacts of agricultural production, residential areas and landfill in An Giang (Area 1), Kien Giang (Area 2) and Can Tho (Area 3), respectively, to assess relationship between water quality and diversity of phytoplankton. The results showed that water quality at 25 study sites is contaminated with organic matters, suspended solids and coliforms. The study found 422 species of phytoplankton belonging to five phyla of Bacillariophyta, Chlorophyta, Dinophyta, Cyanophyta and Euglenophyta. The density of phytoplankton in the three studied areas ranged from 13 to 77,328 individuals L^-1. Among the areas, Area 1 has the highest species composition and density, followed by Area 2 and then Area 3. Among the phytoplankton species occurrence, Melosira granualata, Cyclotella meneghiniana, Cyclotella comta, Trachelomonas sp., Glenodinium beronense, Oscillatoria muticola and Skeletonema costatum dominated and indicated the water environment with high organic matters, nutrient-rich and salty condition. Water quality index (WQI=57-88) indicated water quality ranged from good to medium whereas Shannon-Weiner diversity index (H’=0.71-3.89) showed water quality from medium to heavy pollution. Approximate 56% of the studied sites have similarities in water quality evaluated medium pollution using WQI and H’ although the canonical correspondence analysis (CCA) results indicated that the distribution and abundance of phytoplankton was positively correlated with N-NH₄⁺, P-PO₄^3-, BOD and TSS. It was suggested that H’ is a good water quality indicator for uncontaminated freshwater, but not for saline water or highly complicated contaminating water. The findings revealed that H’ only partially indicates water quality, thus examining physicochemical water quality variables for water quality monitoring is essential