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Climate change is likely to decrease surface water availability in Central Asia, thereby necessitating land use adaptations in irrigated regions. The introduction of trees to marginally productive croplands with shallow groundwater was suggested for irrigation water-saving and improving the land’s productivity. Considering the possible trade-offs with water availability in large-scale afforestation, our study predicted the impacts on water balance components in the lower reaches of the Amudarya River to facilitate afforestation planning using the Soil and Water Assessment Tool (SWAT). The land-use scenarios used for modeling analysis considered the afforestation of 62% and 100% of marginally productive croplands under average and low irrigation water supply identified from historical land-use maps. The results indicate a dramatic decrease in the examined water balance components in all afforestation scenarios based largely on the reduced irrigation demand of trees compared to the main crops. Specifically, replacing current crops (mostly cotton) with trees on all marginal land (approximately 663 km\(^2\)) in the study region with an average water availability would save 1037 mln m\(^3\) of gross irrigation input within the study region and lower the annual drainage discharge by 504 mln m\(^3\). These effects have a considerable potential to support irrigation water management and enhance drainage functions in adapting to future water supply limitations.