Exploitation of the water resources of the Helmand River has been challenging for Iran and Afghanistan. Debates on this issue finally led to a treaty in 1973 between the two countries, in which a total amount of 26 m3/s water from the Helmand River should be delivered to Iran in a normal (or an above normal) water year. The treaty also specifies that a “normal water year” means the year during which the total volume of water at the hydrometric station of Dehrawud (upstream of the Kajakai Dam) is 5661.7 million cubic meter (MCM). This paper aims to assess the long term hydrological conditions of the Upper Helmand River, to detect the occurrence of any non-stationary process in its streamflow time series and compare the possible changes with the content of the 1973 water treaty. Due to very date scarce situation of this region, the SWAT (Soil & Water Assessment Tool) model and CRU (Climatic Research Unit) global dataset were applied to create the long term time series. The results showed that there has been no significant change in annual mean flows in the Upper Helmand River basin. However, there is a consistent increase in monthly flows from November to February and a decrease of the flows in June and July. The monthly changes can be attributed to an increasing trend in temperature in the study area, earlier snowmelts during winter and less snow pack in summer. The applied methodology of this study is useful to cope with the region’s data scarcity and can be applied for similar studies requiring long term time series of hydrological variables.