Abstract Background Population growth and intensified human activities in conjunction with climate variability continue to affect the hydrologic cycle, aquatic and terrestrial flora and fauna. In this regard, understanding interactions among ecosystem functions, impacts of anthropogenic interventions and those of climate variability is vital for projecting future ecosystem responses to human activities and climate forcing. The objectives of this study are to determine the ecological flow state via eco-flow index based on discharge hydrograph, to model the ecological diversity through the Shannon diversity index, and to assess the degree of hydrologic alteration using indicators of hydrologic alteration and range of variability approach in six hydrometric stations along the Zayandeh-Rud River in central Iran. The river drains into Gavkhuni Marsh. Also, the streamflow-induced potential changes for Capoeta damascina (a cyprinid fish species of the genus Capoeta), Petroleuciscus esfahani (a small cyprinid fish) and Aphanius isfahanensis (a Cyprinodontid fish) are evaluated. The outcome is expected to assist managers with understanding the effects of anthropogenic activities and climate variability on Gavkhuni aquatic ecosystems so that management options that enhance species resilience and adaptability are outlined. Results Human activities, a primary factor influencing the natural flow regime, caused a significant increase in the minimum flow, July to March streamflow, low pulse number, and the number of reversals in most studied stations. On the contrary, some other hydrologic indices declined in value. Reservoir impoundment, the most prominent factor among human interventions, resulted in an overall alteration degree of 74.8% in streamflow. Climate variability impacted the natural flow regime in the range of low degree hydrologic alteration (27.3%). In addition, the biodiversity of the study basin, as modeled by the Shannon diversity index, had strong relevance to the annual eco-surplus and was more sensitive to summer floods and autumn hydrological droughts than other factors. Conclusions This study corroborates the effectiveness of scenario-based hydrological modeling framework in evaluating the impacts of climate variability and human activities imposed on natural flow metrics. Additionally, the recently introduced eco-flow metrics based on discharge hydrographs and the Shannon diversity index based on indicators of hydrological alteration may be adopted in basins lacking ecological data. These two indices can effectively identify the most prominent factors in hydrological alteration and biodiversity change through a river network and may provide scientific decision-making support for water resource management in the study area.
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