Water scarcity is an important factor limiting agricultural development in arid areas. Clarifying and evaluating the current situation of water resources in arid regions is helpful for decision-makers in the rational use of water resources. This study takes a typical arid region located at the edge of Taklamakan Desert-Hotan region as the study area. The water footprint (WF) of the Hotan region was calculated based on 20 years of data information from 2000–2019. An evaluation system was established using four aspects of the WF: structural indicators, efficiency indicators, ecological safety indicators, and sustainability indicators. The results show that the WF of the study area is mainly dominated by blue water consumption, with a proportion of 65.74%. The WF of crop production is larger than that of livestock production. The produced WF of grain crops is the highest of all products with a share of 44.21%. The increase in the local agricultural WF reached 53.18% from 2000 to 2019, but it was still lower than the amount of water available for agriculture. The evaluation results indicated that the region’s WF import dependency is lower than the global level, with an annual average self-sufficiency rate of 91.13% and an increase of 878.95% in the WF economic efficiency index. The agricultural WF produced in Hotan is exported in the form of trade, but the quantitative contribution is small and does little to relieve water stress in other regions. The agricultural water consumption was still within the range of local water resources that could be carried but only 6 years of sustainable water use, and the future development was not optimistic. With the ratio of produced WF to available water resources maintained at about 58%, the local available water resources should be above 43.21 × 10⁸ m³ to initially ensure the sustainable use of water resources. There were 12 drought years in the study period, which are prone to droughts and high disaster levels. The drought-water scarcity systems behaved in three phases: 2000–2011 (uncoordinated level), 2012–2015 (transitional phase), and 2016–2019 (coordinated level). Water scarcity threatened by drought reduced. The occurrence of meteorological droughts was more related to natural factors while the changes in WF were mainly driven by socio-economic elements such as human activities.