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Lake evaporation is a critical component of the hydrological cycle. Quantifying lake evaporation in hyper-arid regions by measurement and estimation can both provide reliable potential evaporation (ET0) reference and promote a deeper understanding of the regional hydrological process and its response towards changing climate. We placed a floating E601 evaporation pan on East Juyan Lake, which is representative of arid regions’ terminal lakes, to measure daily evaporation and conducted simultaneous bankside synoptic observation during the growing season of 2013-2015. A semi-empirical evaporation model derived from Dalton model was parameterized and validated with measured data. The model was then used to estimate lake evaporation during 2002-2015. According to in situ measurements, maximum, minimum and mean lake evaporation were 8.1, 3.7 and 6.5 mm/day, and growing season evaporation was 1183.3 mm (similar to 80% of the annual amount). Adding up non-growing season evaporation that we converted from phi 20 pan evaporation at Ejina weather station, the annual mean lake evaporation, 1471.3 mm, was representative of lower Heihe River’s ET0. Model inter-comparison implied our model performed well both in simplicity and accuracy and has potential utilization in a data-sparse area. In 2002-2015, estimated mean daily evaporation was 6.5 mm/day and growing season evaporation was 1233.7 mm. Trend analysis of estimated evaporation proved the evaporation paradox’s existence in this hyper-arid region and validated complementary relationship theory’s adaptability.