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A significant part of the world’s largest river basins are located in areas of arid and semi-arid climate, such as the Amu Darya, Jordan, Murray-Darling, Yellow River, and Aksu-Tarim river basin. These river basins are experiencing water scarcity resulting in conflicts between upstream and downstream, conflicts between water users, and degradation of the natural ecosystems. Therefore, in many river basins, including the Aksu-Tarim river basin, water quota systems have been established, in order to allocate water under scarcity. The Aksu-Tarim river basin (NW China) has developed into one of the most important cotton production areas worldwide. In this paper, we aim at assessing the water consumption through irrigated agriculture, mainly cotton, and natural vegetation in the Aksu-Tarim river basin against the background of this water quota system. Firstly, we map the evapotranspiration (ETa) as water consumption of irrigated agriculture and natural vegetation in the Aksu-Tarim river basin. Secondly, we calculate water balances and relate them to the water quota system. We employed the remote sensing method Simplified Surface Energy Balance Index (S-SEBI), in order to map ETa based on MODIS satellite images for the growing seasons 2009, 2010, and 2011. Thereby, the MODIS products 8-day land surface temperature (MOD11A2), 16-day albedo (MCD43A3), and 16-day NDVI (MOD13A1) were used. The ETa of cotton ranges from 884 to 1198 mm. The ETa of the natural vegetation of a total coverage ranges from 715 in 2009 to 960 mm in 2011, clearly following the annual runoff of the Aksu and Tarim River. The water balance of the Aksu-Tarim river basin is -3.25 to -3.73 km(3), 0.1-0.53 km(3), and -3.55 to -4.12 km(3) in 2009, 2010, and 2011, respectively. The water quotas along the Aksu River and the upper reaches of the Tarim are exceeded by water consumption, while the quotas along the middle and lower reaches are not met Considerable amounts of groundwater, including fossil groundwater, are exploited for irrigation along the Aksu and Tarim River, which must be regarded as exploitation of a non-renewable resource. (C) 2014 Elsevier Ltd. All rights reserved.