Since the impoundment of the Three Gorges Dam, 50% of the first-order tributaries in the reservoir area have had frequent algal blooms but with variations regarding the geographical locations of the seriously bloomed sections and the scope of the latter being influenced by the mainstream. This study took the Pengxi River, a first-order tributary of the reservoir area, as an example in order to explore the difference in eutrophication among the river sections and the influence of the Yangtze River on its tributaries. During the spring bloom season of 2019, sampling was carried out in one-week intervals for a total duration of one month. Seven sampling sections (PX1-PX7) were set up from the confluence to upstream. According to the profiles of vertical water temperature and conductivity of each section, the influence scope and form of the backwater of the Yangtze River were inferred; in addition, severity differences and mechanisms of algal blooms among sections were explored through the comparison of the hydrology, water quality, and sediment nutrients among Gaoyang Lake (PX5), which has had serious algal blooms, and the upstream (PX6) and downstream (PX4) sections of PX5, which are both 4 km away from PX5. The results showed that during the sampling month, the average ρ (Chl-a) in the confluence area of the Pengxi River (PX1-PX4) and in the upstream (PX5-PX7) were in the range of 14.55-44.00 μg·L -1 and 42.66-175.40 μg·L -1 , respectively. The ρ (Chl-a) of PX5 was up to 413.00 μg·L -1 , which was significantly higher than that of other sections ( P <0.05). Temperature and conductivity results showed that the backwater from Yangtze River flowed into the Pengxi River from the middle and bottom layers during the period from April to May. The confluence (PX1-PX4) sections were in the intersection area of the backwater from Yangtze River and the upstream of the Pengxi River; thus, the waterbody was unstable, which was not conducive to the formation of algal blooms. However, the upstream (PX5-PX7) sections were not directly affected by the backwater from Yangtze River, leading the nutrient exchange mainly vertically. Most averages of n (TN)/ n (TP) and n (DTN)/ n (DTP) of PX4-PX6 were all greater than 16, indicating a phosphorus-limited state. During sampling, the average sediment total phosphorus of PX5 was 91% of that in upstream PX6, which was only 4 km away, whereas the surface water total phosphorus of PX5 was 180% of that in PX6. The important reason for this phenomenon is that the water surface width of PX5 was 3.6-4.7 times that of PX6, indicating longer wind fetch in the former section. Owing to the mountainous landscape in the Three Gorges Reservoir (TGR) region where windy weather is rare, the disturbance effect of wind and waves on PX5 was stronger than that of PX6, and the nutrients released from the sediment at the PX5 section caused by wind and waves resupplied the surface water more easily, causing more serious algal blooms at PX5 than those at the remaining sections in the Pengxi River. The main causes of the algal blooms in the tributaries of the TGR area lied in the stability of water stratification and the supply of internal phosphorus. The stability of water stratification was mainly affected by the backwater from Yangtze River, and the supply of internal phosphorus in the algal bloom season was affected by the special water stratification phenomenon of the tributaries of TGR-the "surface density layers." The duration and degree of weather disturbance to the surface density layers can be used to predict the time and scale of algal blooms.