Phytoplankton community characteristics and associative primary productivity, which reflect the ecological and nutritional status of water, are sensitive to environmental change. Particularly, nutrient inputs have a significant effect on phytoplankton growth and development as well as the biogeochemical cycle of watersheds. We investigated the phytoplankton community and nutrient status downstream from the Gan River into Poyang Lake. On a catchment scale, the phytoplankton communities and associative primary productivity from these two water bodies differed. The Poyang Lake phytoplankton community is composed of seven phyla of algae, whereas the Gan River is composed of six, the dominant phyla of phytoplankton being Bacillariophyta and Cryptophyta in Poyang Lake and Gan River, respectively. Phytoplankton abundance and primary productivity were significantly higher in Poyang Lake. Lower nitrogen (N) and phosphorous (P) concentrations and higher carbon (C) and silicon (Si) concentrations significantly affected the phytoplankton communities and primary productivity distribution in the entire Poyang Lake Basin. In this regard, we found a significant correlation between the phytoplankton community of the Gan River and P and N, whereas N and Si primarily regulated the phytoplankton community structure of Poyang Lake. Moreover, we found a significant correlation between DTN, Si/P, DIC/P, and primary productivity in the Gan River, whereas NH4+ jointly controlled primary productivity in Poyang Lake. Furthermore, the Margalef Richness Index (0.84-2.41) can be indicative of the environmental water quality status; and we determined that the most area of Poyang Lake and Gan River both were P restriction and moderately polluted, whereas the entrance of the Gan River into Poyang Lake was seriously polluted, which confirms that the Gan River is a main and crucial source of Poyang Lake pollution. Nanjishan Nature Reserve was already slightly eutrophic due to the high nutrient content and a large number of algae in the south-east of Poyang Lake, but the Gan River had good river fluidity, so some areas of the Gan River were oligotrophic.
