Abstract: In order to reveal the impact of aqua farms on the water environment in the Ganjing River of the Three-Gorge Reservoir, we investigated the community structure of the phytoplankton and tested the physyco-chemical parameters of the water at four sampling sites in the Ganjing River in different seasons. We applied regular methods and collected water samples in March, June, September and December of 2013. We observed 93 phytoplankton species that belonged to seven phyla. The dominant phylum was Chlorophyta (37 species), followed by Bacillariophyta (26 species) and Cyanophyta (13 species), and these three phyla accounted for 39.79%, 27.96% and 13.98% of the entire sample. The average annual abundance of the phytoplankton was 7.58106 cells/L, ranging from 3.06 to 5743.99104 cells/L. The average annual biomass was 4.40 mg/L, ranging from 0.03 to 17.67 mg/L. The average annual Secchi-depth (SD), chlorophyll-a, total phosphorus (TP) and total nitrogen (TN) were 1.18 m, 8.54 g/L, 0.127 mg/L and 1.95 mg/L respectively. The mean Shannon-Weiner diversity index was 2.90, ranging from 1.11 to 4.17. The average annual Pielou evenness index was 0.88, ranging from 0.34 to 1.49. The comprehensive trophic level index of the Ganjing River was between 37.59 and 71.86 with an average of 56.71. The water quality of the Ganjing River was evaluated to be eutrophic and mesotrophic. The water quality of the aquaculture area was better than the other areas in June when fishes grew rapidly, and in other months, there was no obvious difference in the water quality between the aquaculture area and the other areas. This suggested that the filter-feeding fishes might moderately improve the biodiversity and the water quality.