This Regular evaluation and analysis of river quality helps accurate management to reach acceptable quality. In this study, water quality indices (WQI) method applied to evaluate quality of Jajrood River which is one of the main sources of Tehran drinking water. It helps to subsidize management actions in Jajrood watershed. Sampling carried out for 9 years during 2001-2010 in 10 stations along the river in wet and dry stations to identify water quality and the main source of pollution. Results show water quality in all stations classifies as medium according to National Sanitation Foundation (NSF) and water quality index in wet season is better than the corresponding value in dry seasons. Entrance of pollution during the upstream of Latian Dam (especially in populated centers) has negative effect on the water quality, however river has a good natural attenuation capacity, therefore quality index of river in the main inlet of Latian dam (Lashkarak Bridge) classifies as medium. Collecting wastewater at the populated centers and developing soil conservation and controlling erosion at the upstream of watershed can effectively improve the water quality of river.