Chlorophyll a, as an important water quality indicator, can intuitively describe the nutritional status of the water. During the transportation with water, the concentration of chlorophyll a in the water will change correspondingly under the influence of environmental factors along the way. From November 2017 to October 2018, we set up fixed sampling sites along the East Taihu Lake and Taipu River to carry out monthly investigation and analysis on the chlorophyll a of the water. The results showed that the concentration of chlorophyll a from the East Taihu Lake to the sites along the Taipu River had a significant longitudinal variation. The annual average concentration of chlorophyll a in East Taihu Lake was (15.341±2.329) μg/L. After passing through several sites of the Taipu River, the concentration reached (11.002±1.004) μg/L at the site of Jinze Hydrological Station, which showed a significant decline trend overall (P<0.05). There were differences in the contrast characteristics between every two different sites. The longitudinal variation characteristics also appeared differences in the different months. Clustering and nMDS analysis also presented the differences among the different sites and the different months. Nonlinear regression analysis revealed that the environmental factor which appeared the highest correlation with chlorophyll a concentration was the light intensity at 0.5 m below water surface (P<0.01), and the chlorophyll a concentration was also significantly correlated with the dissolved oxygen in October 2018 (P<0.05). According to the currently existing studies, the longitudinal variation of chlorophyll a in water is influenced by many factors such as water quality. In the future, more environmental factors should be considered, and the comprehensive effects of water quality, precipitation, hydraulic retention time, current velocity and runoff on the temporal and spatial distribution characteristics of chlorophyll a should be analyzed systematically, which can provide the scientific basis for the safeguard on the water quality of the water sources.