Abstract: In order to select asuitable method for water quality evaluation in the Pearl River Delta (PRD), we accessed and analyzed the water environment factors and phytoplankton data in PRD in 2015. Four phytoplankton indices, including Shannon index, evenness index, richness index and biomass index, were selected from six common phytoplankton indices based on similarities by using self-organizing map (SOM). Then, we compared the water quality evaluation results of the above indices and environmental factors. The results based on dissolved oxygen and ammonia nitrogen could reflect the spatial differences between city centers and other regions, but total nitrogen and total phosphorus were not suitable for water quality evaluation. However, the results based on Shannon and biomass indices could reflect the differences between city centers and other regions, but evenness and richness indices were not suitable for water quality evaluation. Except for total nitrogen and total phosphorus, the evaluation results of other environmental factors and four phytoplankton indices show that the water quality of the survey area was generally good, but the water quality of stations around the city was slightly poor. Thus, issolved oxygen, ammonia nitrogen, Shannon index and biomass index are suitable environmental factors and phytoplankton index for water quality evaluation.