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In order to explore new bioindicators of aquatic environments, phytoplankton functional groups (FGs) were applied in a subtropical estuarine river delta system (the Pearl River Delta) for 2012 and 2015. Our results showed that the water quality (physicochemical parameters) of 2015 was better than 2012, which was benefited from Chinese government’s implementation of water pollution control measures. However, a non-metric multidimensional scaling analysis (NMDS) based on phytoplankton FGs similarities did not show interannual differences correspondingly. This implied that the present improvements in water quality were insufficient to affect the interannual alterations of FGs. Among the 29 FGs identified, FGs P and TB were predominant in biomass, with sum proportion of 75%, while other FGs showed occasional advantages either seasonally or spatially, reflecting their randomness of exogenous inflows from water bodies such as lakes and reservoirs. The diversity of dominant FGs could be good bioindicators to spatial and seasonal variations in water quality, since it showed apparently lower in high eutrophic conditions (around Guangzhou city or dry seasons), and higher when water quality was better (the West River side or wet seasons). Therefore, we assumed that continued efforts in improving water quality would finally enhance the diversity of dominant FGs in the study area. In conclusion, the phytoplankton FGs method is suitable for identifying the spatial and seasonal characteristics of aquatic environments greatly affected by human activities, but its sensitivity to interannual water quality improvements requires further investigation.