After the impoundment of the Three Gorges Dam for more than 20 years, over 50% of 1_st ^{order tributaries have experienced} harmful algal blooms (HABs), primarily dominated by Dinoflagellates, Cyanobacteria and Green Algae. Investigating the relationship between HABs and endogenous nutrient accumulation will help in the early warning of HABs and in predicting the ecological environment in the Three Gorges Reservoir (TGR). The sediment cores are undoubtedly valuable materials for studying the effects of internal nutrient accumulation and algal bloom impacts. This study selected two 1_st ^order tributaries both mainly located in Yunyang County of the TGR, namely Pengxi River which have been heavily algal bloomed, and Modao River barely reported with bloom. Sediment cores were collected from both mid-reaches to investigate the effects of blooms on sediment deposition under similar climatic and geographic conditions. Through the ₂₁₀^{Pb dating methods}, the sedimentation deposition depths after TGR impoundment in Pengxi and Modao River were 45cm and 30cm, with average sedimentation rates of 2.3 and 1.5cm.a_-1^{, respectively,} showing Modao River was only 65% of Pengxi River in this rate. The sediment cores show that prior to impoundment of TGR, the average contents of organic matter (OM), TN, TP, Available Phosphorus (AP), and Alkali-hydrolyzable Nitrogen (AN) in Pengxi River sediments were 9154.9, 454.1, 432.1, 13.3, and 60.4 mg.kg?1, respectively; in Modao River, the respective values were 12342.4, 756.5, 530.2, 17.0, and 63.2 mg.kg?1, which were 35%, 67%, 23%, 28%, and 5% higher than those in Pengxi River. As of the 2023 layer in the core, OM content in Pengxi and Modao River sediments was 19182.2 and 13878.6 mg.kg?1, respectively, with the latter being only 72% of the former. TN, TP, AP, and AN in Pengxi River sediments increased by 96%, 37%, 77%, and 51%, respectively, compared to its pre-impoundment levels, while Modao River showed increases of 16%, 13%, 8%, with AN decreasing by 2% based on the similar relative comparison. The results of 16S and 18S DNA high-throughput sequencing of 5 cm sections from the top 20 cm of the sediment cores revealed no significant differences in the microbial community composition between the two rivers. However, combining core dating, surface DNA sequencing and phytoplankton community data during bloom periods indicated that between 2010 and 2023, the relative abundances of Dinoflagellates and Green Algae in the 0~5 cm layer of Pengxi River cores increased by 2.1 and 0.1 times, respectively, compared to the 15~20 cm layer. Conversely, in Modao River during the same period, Dinoflagellates and Green Algae relative abundances decreased by 50% and 70%, respectively. A significant positive correlation was found between the relative abundance of Dinoflagellates and organic matter in both rivers" sediment cores (P<0.05), suggesting that Dinoflagellate blooms are the primary cause of the differences in endogenous organic matter deposition post-impoundment. As endogenous organic matter accumulates, the risk of future algal blooms, especially Dinoflagellate blooms, in the 1^_st order tributaries of TGR will increase. Organic matter content and the dynamics of endogenous nutrient accumulation in sediments could serve as key indicators for predicting the future scale of Dinoflagellate blooms in the tributaries of the reservoir.