In this study, we proposed an approach to recommend environmental flows in highly regulated areas, considering the multiple time scales of hydrological processes and water requirements. Water resources were seasonally allocated to the agricultural sector using a benefit-maximizing model, based on water deficiency at different crop growth stages. The economic feedback was evaluated after securing different levels of initial environmental flows. The final environmental flows were recommended to maintain a balance between the ecosystem and irrigation water needs. A case study was applied in the Baiyangdian watershed, China. The results show that a benefit-maximizing model can reduce the total economic losses to the maximum potential, which contributes to alleviating water use conflicts between agriculture and the ecosystem. However, the environmental flows cannot be maintained without the sacrifice of production losses, except for in extremely wet years. Average environmental flows could be secured at around 3.1, 4.3 and 5.4 × 108 m3 in dry, average, and wet years, respectively, with less than 10% production loss. Additional water transfer projects, as well as economic compensation strategies, are suggested to meet both ecosystem and agricultural needs. The planned economic compensation during 2010-2015 was 16.3 × 108 Yuan, giving priority to securing environmental flows, and accounting for 7% of the total agricultural output value. The suggested amount of water resource transferred by the South-to-North Transfer Projects was 19 × 108 m3, which is enough to alleviate water use conflicts between different stakeholders in dry years. This study provided a method to protect ecosystems in a more sustainable way.