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Due to global warming, there is a need to increase the water use efficiency of crops under rainfed agriculture, particularly in semi-arid regions. Therefore, the effect of NPK fertilizer application (with or without liming) on the water use efficiency of a maize/cowpea intercropping system was investigated in the semi-arid part of Brazil. The crops were grown on a strongly acidic, sandy soil with three treatments: (i) Complete NPK fertilizer application with lime (Compl), (ii) Complete NPK fertilizer application without lime (Compl-L) and (iii) Control. On the average, dry matter production was 2.6 times higher with the Compl treatment than in the Control and 1.6 times higher than in the Compl-L treatment. The soil water balance was calculated with two different model approaches (HILLFLOW and EPICSEAR). When checked against measured soil water content during the growing period, both models produced accurate results, but only EPICSEAR was sensitive to the effects of liming and fertilizer application on soil water balance and dry matter production at this site. Comparison between the Compl and the Compl-L treatments shows that the increase in transpirational water use efficiency (WUET) (+63 and +80%, respectively) is mainly due to the application of NPK. Although the site is highly acid, liming was of minor importance for increasing the WUET. However, observations and simulations demonstrate that, through the additional application of lime, the gross water use efficiency (WUEC) in a maize/cowpea intercropping system can be increased by 60% compared to sole application of NPK and by more than 160% compared to the control.