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Capillary rise represents an often neglected fraction of the water budget that contributes to crop water demand in situations of shallow groundwater levels. Such a situation is typical in irrigated areas of Central Asia where water from capillary rise is exploited by farmers to meet production targets in Uzbekistan under uncertain water supply. This leads to higher water inputs than needed and creates a vicious cycle of salinization that ultimately degrades the agricultural land. In this study, capillary rise is quantified at different spatial scales in the Shomakhulum Water Users Association (WUA), situated in the southwest of Khorezm, Uzbekistan. The mathematical model HYDRUS-1D was used to compute the capillary rise at field level for three major crops (cotton, wheat and vegetables) on six different hydrological response units (HRUs). These six HRUs having homogenous groundwater levels (1–2 m beneath the soil surface) and soil texture were created using GIS and remote-sensing techniques. Capillary rise from these HRU was then up-scaled to WUA level using a simple aggregation approach. The groundwater levels simulated by FEFLOW-3D model for these HRUs in a parallel study under four improved irrigation efficiency scenarios (S-A: current irrigation efficiency or business-as-usual, S-B: improved conveyance efficiency, S-C: increased application efficiency and S-D: improved conveyance and application efficiency) were then introduced into HYDRUS-1D to quantify the impact of improved efficiencies on the capillary rise contribution. Results show that the HRUs with shallow groundwater-silt loam (S-SL), medium groundwater-silt loam (M-SL) and deep groundwater-silty clay loam (D-SCL) have capillary rise contribution of 28, 23 and 16 % of the cotton water requirements, 12, 5 and 0 % of the vegetable water requirements and 9, 6 and 0 % for the wheat water requirements, respectively. Results of the scenarios for the whole WUA show that the maximum capillary rise contribution (19 %) to the average of all crops in the WUA was for the S-A scenario, which reduced to 17, 11 and 9 % for S-B, S-C and S-D, respectively. Therefore, it is recommended that before any surface water intervention or drainage re-design, water managers should be informed about the impacts on groundwater hydrology and hence should adopt appropriate strategies.