Study region The Zayandehroud River, located in central Iran, is a highly regulated watercourse within a semi-arid basin. Intensive upstream interventions, including dam construction, inter-basin transfers, and extensive water withdrawals, have altered the natural flow regime, resulting in the degradation of downstream aquatic ecosystems and increased ecological stress. Study focus This study applies four environmental flow (EF) assessment methods, the modified Tennant method, wetted perimeter method, ecological hydraulic radius method, and habitat simulation using HEC-RAS. Flow naturalization is employed to reconstruct pre-regulation flow regimes, thereby enhancing the accuracy of hydrological and hydraulic approaches. To assess method suitability, two new metrics, failure index and damage severity index, are introduced. New hydrological insights for the region Findings reveal that the ecological hydraulic radius method, which incorporates species-specific velocity requirements, yielded the most reliable EF estimates compared to habitat simulations. Optimal ecological flows, estimated at similar to 37 % of the mean annual natural flow, far exceed current allocations, underscoring the ecological cost of overuse. The modified Tennant method, when applied to naturalized flows, provides a practical baseline for EF provision. Overall, results emphasize the critical role of flow naturalization in improving EF assessments and support ecologically grounded water management in arid and semi-arid regulated rivers.