In order to know more about the change of water quality, phytoplankton's community structure and the evolution of river ecosystem by human activities. In June 2019, the phytoplankton samples and water samples were collected from 21 locations in three rivers with different nutrition levels, which included Jinjiang River, Xiangjiang River and Nanming River. Physicochemical factors, species composition and abundance of phytoplankton were studied, and combined with the result of Redundancy analysis (RDA) studied the relationship of these indexs, the spatial distribution characteristic of phytoplankton was analyzed using the clustering analytical method simultaneously. The results showed that the eutrophication level of the three rivers were in order of Nanming River > Xiangjiang River > Jinjiang River, the comprehensive trophic level index (TLI) of the three rivers were 61.76, 48.76 and 36.05, respectively. Twenty-one species of 19 genera in 6 phyla phytoplankton were found in Jinjiang River, in which Bacillariophyta was the predominant species, and accounted for 57.14% of the total species. Forty-three species of 34 genera in 6 phyla phytoplankton were found in Xiangjiang River, in which Bacillariophyta and Chlorophyta were the predominant species, accounted for 41.86% and 37.21% of the total species respectively. Forty-six species of 32 genera in 6 phyla phytoplankton were found in Nanming River, in which Bacillariophyta and Chlorophyta were the predominant species, accounted for 39.13% and 32.61% of the total species respectively. The cell density of phytoplankton in water sample of Jinjiang River, Xiangjiang River and Nanming River were 12.66×10⁵ cells/L, 38.66×10⁵ cells/L, and 132.61×10⁵ cells/L, respectively. The cell density of phytoplankton was positive correlation with dissolved oxygen (P<0.05), and it was positive correlation with conductivity, total dissolved solids (TDS), salinity, total nitrogen, total phosphorus, ammonia nitrogen, and nitrate nitrogen (P<0.01). The conductivity, salinity, TDS, and nutrient concentration in Jinjiang River were the lowest, however, these indexes in Nanming River were the highest. The result from hierarchical cluster analysis showed that community structures of phytoplankton in the three rivers were different, and these samples were divided into two groups, in which the samples of Jinjiang River and Xiangjiang River were one group, the samples of Nanming River were the other group. These studies suggested that with the intensifying of human activity, the conductivity, salinity, TDS, nutrient concentration and phytoplankton abundance in rivers increased, the abundance of Bacillariophyta decreased, otherwise, the abundance of Cyanophyta increased.