Water samples were collected by using standard methods at ten locations in Yi River watershed from July 2006 to May 2007. Yi River watershed contains 181 species and varieties, 73 genera, and 7 divisions of phytoplankton, among which Chlorophyta and Bacillariophyta are the most important component. Within the watershed, there are 137 species and varieties, and 7 divisions of phytoplankton in Yi River; 134 species and varieties and 7 divisions in Beng River; 75 species and varieties, and 7 divisions in Dongwen River; 67 species and varieties, and 6 divisions in Meng River; 70 species and varieties, and 6 divisions in Su River; and 80 species and varieties, and 7 divisions in Liuqing River. Water quality assessment was calculated by using saprobic indicator, saprobic indicator commuuity, and phytoplankton general index. Overall evaluation result of Yi River watershed water quality is: Dongwen River, Su River, Meng River, Beng River and Yi River are β-ms, and Liuqing River is α-β-ms. The water quality orders are: Su River> Dongwen River> Beng River> Yi River> Meng River> Liuqing River. Building rubber dams has changed the rearrangement of the water yield in Yi River and Beng River, which has reduced their streams speed greatly and caused the change of phytoplankton community from fluvial facies to the lake facies. However, it has less effect on Dongwen River, Meng River, Su River and Liuqing River, relatively.