After the impoundment of the Three Gorges Reservoir for more than 20 years, over 50% of first-order tributaries have experienced harmful algal blooms (HABs), primarily dominated by cyanobacteria, green algae and dinoflagellates. Investigating the relationship between HABs and endogenous nutrient accumulation can help in early HAB warning and ecological predictions in the Three Gorges Reservoir. Sediment cores are invaluable for studying internal nutrient accumulation and its impact on HABs. This study focused on two first-order tributaries in Yunyang County of the Three Gorges Reservoir—the Pengxi River, frequently impacted by HABs, and the Modao River, with rare occurrences of HABs. Sediment cores were collected from the mid-reaches of both rivers to investigate the effects of HABs on sediment deposition under similar climatic and geographic conditions. Using 210Pb dating, sediment deposition depth after Three Gorges Reservoir impoundment was 45 cm for Pengxi River, with a sedimentation rate of 2.25 cm/a. In contrast, sediment deposition depth in Modao River was 30 cm, with a sedimentation rate of 1.50 cm/a—only 65% of the sedimentation rate in the Pengxi River during the same period. The sediment core data showed that before the impoundment, the sedimentation fluxes of organic matter(OM), total nitrogen(TN), total phosphorus(TP), available phosphorus(AP), available nitrogen(AN) in the sediment of Pengxi River were 13.35, 0.81, 0.61, 0.01 and 0.02 g/(m²·a), respectively, while in Modao River, they were 12.90, 0.79, 0.54, 0.01 and 0.01 g/(m2·a), respectively. As of 2023, after the impoundment, the sedimentation flux of OM in Pengxi River and Modao River were 25.95 and 14.32 g/(m²·a), respectively, with the latter being only 55.18% of the former. In Pengxi River, the sedimentation fluxes of OM, TN, TP, AP, and AN increased by 94.38%, 53.09%, 31.15%, 77.78%, and 55.56%, respectively, compared to pre-impoundment levels, while in Modao River, the increases were only 11.01%, 13.92%, 16.67%, 7.19%, and -2.17%, respectively. The 16S and 18S DNA high-throughput sequencing was performed on samples collected at 5 cm intervals from the top 20 cm of sediment cores from Pengxi River and Modao River. The results showed no significant difference in the prokaryotic community composition. However, in terms of eukaryotic communities, the sediment core from Pengxi River exhibited higher biodiversity and species richness compared to the sediment core from Modao River. Combining sediment core dating, nutrients, and sequencing data, the analysis revealed that from 2010 to 2023, the relative abundance of dinoflagellates and green algae in the 0-5 cm section of the Pengxi River sediment core increased by 208% and 9%, respectively, compared to the 15-20 cm section. In contrast, their relative abundances decreased respectively by 50% and 70% in Modao River. Correlation analysis showed that the relative abundance of dinoflagellate in the sediment core was significantly positively correlated with OM, while the relative abundance of green algae was significantly positively correlated with TP and AP. It suggests that dinoflagellate blooms are the primary cause of the differences in endogenous OM deposition between the two rivers after impoundment, while green algae blooms are related to the accumulation of endogenous phosphorus. Studies on sediments and HABs have demonstrated that Three Gorges Reservoir impoundment has enriched Pengxi River with nutrients, intensifying HABs frequency and scale while significantly influencing internal nutrient accumulation. Endogenous OM accumulation indicates an increasing risk of HABs, particularly dinoflagellate blooms, in primary tributaries of the Three Gorges Reservoir. OM and endogenous phosphorus in sediments can serve as key indicators for predicting HAB scales in Three Gorges Reservoir tributaries.