Abstract: To investigate the hydrodynamic characteristics of the Danjiangkou Reservoir and their potential impacts on algal blooms, this study developed a three-dimensional hydrodynamic model based on the EFDC method. The flow field evolution under multi-condition operation, including the Taocha water diversion, dam discharge, and inflow from the Hanjiang sub-reservoir were systematically simulated, and quantitatively assessed the hydrodynamic improvement effects. Results indicate that: ① The Danjiang sub-reservoir exhibits low overall flow velocity with moderate spatial variation. Its surface wind-driven circulation structure remains stable, showing an average velocity increase of approximately 0.3 cm/s under various operational conditions, revealing limited improvement. In contrast, the Hanjiang sub-reservoir features a stable flow field structure that is sensitive to flow rate changes, coupled with significant spatial heterogeneity in flow velocity. Under short-term high-flow impacts, its average velocity increases by about 10 cm/s, demonstrating a significant overall improvement effect. ② Reservoir flow fields are jointly driven by wind-induced currents and throughput flows. Wind-induced currents are the decisive factor shaping the flow field pattern in the Danjiang sub-reservoir, while throughput flows, comprising inflow from the Hanjiang sub-reservoir, diversion from the Taocha Canal, and dam releases, are key to controlling hydrodynamics in the Hanjiang sub-reservoir. ③ Conventional water diversion struggles to effectively enhance Danjiang sub-reservoir′s flow dynamics; algal bloom prevention should prioritize localized early warning systems and ecological measures. The water environmental capacity of Hanjiang sub-reservoir can be directly and efficiently increased through optimizing ecological discharge flows and other operational adjustments. These findings can provide scientific evidence and theoretical support for reservoir water quality assurance and ecological flow management.