The Yellow River (YR) is the second-longest river in China and the cradle of Chinese civilization. It supports hundreds of millions of people across nine provinces and autonomous regions, sustaining agriculture, industry, and urban water supply throughout China's arid and semi-arid interior. Decades of intensive water extraction, rapid urbanization, and large-scale hydraulic infrastructure construction have profoundly degraded the river's ecological integrity, including the recurrent flow cessation events documented in the lower reaches during the 1990s. A major challenge in evaluating environmental flows (E-flows) in the Yellow River Basin (YRB) is reconciling naturalized flow reconstruction with the extensive regulatory modifications imposed by major reservoirs, including Longyangxia, Liujiaxia, Sanmenxia, and Xiaolangdi. To address this challenge, we constructed and calibrated an HEC-HMS hydrological model using meteorological data from the Climate Research Unit (CRU). The model reconstructs naturalized streamflow at 29 stations distributed across the main stem and major tributaries of the YRB from 2004 to 2024. Four established hydrological methods were applied to estimate Eflows: the Tennant method, the low-flow index (7Q10), flow duration curve analysis (Q90 and Q95), and flow duration curve shifting (FDCS). An ensemble mean was computed to reduce method-specific bias. The results indicate that, on average, E-flows represent approximately 35% of the naturalized mean annual flow (NMAF), with method-specific estimates ranging from 25% (Q95) to 46% (FDCS). Seasonal analysis reveals that both low-flow (October-March) and high-flow (April-September) seasons partially satisfy minimum ecological requirements in the upper and middle reaches; however, downstream reaches particularly those traversing major urban agglomerations such as Zhengzhou, Kaifeng, and Jinan exhibit severe ecological degradation. The findings yield new insights for riverine ecology management and provide a scientific foundation for sustainable water resource planning in China's Yellow River Basin.