This study focuses on two main indicators—"climate change" and "Afghanistan’s hydropolitical policies"—to analyze the state of water resources in the Helmand River Basin. The aim is to examine the climatic impacts over the past three decades (1991–2021) in the basin, as well as to evaluate the consequences of Afghanistan’s hydropolitical policies (such as dam construction, river diversion, etc.) on water resource reduction, food security, migration, and transboundary tensions with Iran. The research methodology employs an integrated quantitative and qualitative approach, including analysis of climatic data, the SPEI drought index, satellite data, and spatial and geopolitical analyses. The innovation of this study lies in integrating climatic data with spatial and geopolitical analyses and using the SPEI index for a comprehensive assessment of water security in a transboundary basin. The findings indicate that, during the years 1991 to 2021, climate change in the Helmand River Basin has led to a significant decrease in precipitation, rising temperatures, increased evaporation, and intensified drought. These developments have seriously threatened the sustainability of water resources, agriculture, and the Hamoun wetlands. In addition, the results show that Afghanistan’s hydropolitical policies, including the construction of large dams such as Kajaki and Kamal Khan, as well as river diversion projects, have been designed and implemented in the context of hydropolitical competition with Iran and to increase Afghanistan’s water hegemony. These actions have resulted in a sharp reduction in water inflows to Sistan Plain, threatened food security, destroyed ecosystems, and increased migration, with extensive environmental, economic, political, and social consequences, especially in Iran’s border regions. Moreover, the continuation of this trend will significantly intensify hydropolitical tensions between the two countries.