The hydrodynamics and environmental factors in the Xiangxi River (XXR) and Shennong River (SNR), which are tributaries of the Three Gorges Reservoir (TGR), were monitored from July to August (the low water level period) and in October (the impoundment period) in 2018. The vertical distribution characteristics of chlorophyll a and other indicators of the two tributaries were analyzed during the different operation periods, and the factors that affected the vertical distribution in each period were discussed. The results showed that the vertical distribution of dissolved oxygen, water temperature, pH value, and chlorophyll a of the XXR and SNR during the low water level period was relatively consistent. The indexes 0-10 m (0-5 m for chlorophyll a) from the surface of the XXR and SNR, respectively, showed significant stratification and decreased with increasing water depth; the stability index of thermal stratification (RWCS/H) was 13.71-29.07 m-1, which was stable. After the water depth reached 10 m (5 m for chlorophyll a), the indexes tended to be stable along the water depth. During the impoundment period, there was no obvious stratification for each index; the stability index of thermal stratification was 0-0.5 m-1, the stability of the water body was weak, and the vertical variation of each index was relatively stable. The comprehensive trophic state index (TLI) of the XXR and SNR were 55 and 53 during the low water level period, respectively, indicating that they were in a slightly eutrophic state, and 39 and 46 during the impoundment period, respectively, indicating a mesotrophic state. Linear regression analysis showed that chlorophyll a, dissolved oxygen, water temperature, and pH in the two tributaries were significantly correlated in the vertical direction in the low water level period, indicating that dissolved oxygen, water temperature stratification, and pH were important factors affecting the vertical distribution of chlorophyll a. During the impoundment period, a large amount of backflow from the Yangtze River, a large fluctuation in tributary water level, and the decrease in RWCS/H were the important factors that affected the small vertical change in the water body. The enhancement of vertical mixing and the decrease in Zeu/Zmix were the key factors affecting the nutritional status of the water.