Low flow is one of the most effective hydrologic parameters in aquatic ecosystems, power production, reservoir, management and industry. Occurrence of severe low flows have a lot of effects on drinking water supply, water quality, navigation, agriculture and so on and this will make a lot of problems. Changing in characteristics of low flows (depth, frequency and duration) in future affected by climate change, may have important effects on various aspects of Socio-economic, environmental, water resources and governmental planning. Therefore, it is necessary to investigate the changes in this parameter in future periods under effective factors such as climate changes. In this regard, this research examines low flows in future under the effects of climate changes in the upstream of Zayanderood basin considering the uncertainty related to various low flow indices. In this study, nine hydrometric and meteorological stations were considered in order to investigate the effects of climate changes on low flows in future periods 2016-2045 and 2046-2075. As AOGCM models in studies of the impacts of climate changes are an important source of uncertainty, scenarios of temperature and precipitation using 5 atmospheric general circulation models including BCM2.0, CSIROMK3.0, GFDLCM2.1, HADCM3 and MRI CGCM2.3.2 was prepared under A2 and B1 emissions scenarios. Then the LARS-WG model were used for downscaling temperature and precipitation scenarios. Also, the SWAT hydrologic model were considered in order to simulate daily flows in future period. The noted model, after calibration and verification by observed flow, was simulated daily flows in the future period for each hydrometric stations using downscaling temperature and precipitation scenarios. Data of daily flows were used to extract low flow indices in the observed period and the future periods 2016-2045 and 2046-2075. The indices in this research are used for assessing climate changes impacts including indices extracted from flow duration curve (Q90 and Q95) and also from annual minimum flow series (Q(7,2), Q(7,10) and Q(7,20)). Results indicate increasing and decreasing changes in indices under various scenarios. Based on the result of 5 atmospheric general circulation models, the conditions of low flows in future, in upper half of the study area (Eskandari and Zayanderood hydrometric stations) will be better but low flow indices decrease in the lower half of the study area (Ghaleshahrokh and Chelgerd hydrometric stations). According to ideal scenarios, the conditions of study area are more satisfactory in the future. But according to median and critical scenarios, the condition of study area is inappropriate in the future. The observed changes in low flow conditions are based on future temperature and precipitation scenarios. Key words : climate change, low flow, atmospheric general circulation models, downscaling, SWAT model, LARS-WG model, Zayanderood basin