Spatial-temporal information of different water resources is essential to rationally manage, sustainably develop, and optimally utilize water. This study focused on simulating future water footprint (WF) of two agronomically important crops (i.e., wheat and maize) using deep neural networks (DNN) method in Nile delta. DNN model was calibrated and validated by using 2006-2014 and 2015-2017 datasets. Moreover, future data (2022-2040) were obtained from three Representative Concentration Pathways (RCP) 2.6, 4.5, and 8.5, and incorporated into DNN prediction set. The findings showed that determination-coefficient between historical-predicted crop evapotranspiration (ETc) varied from 0.92 to 0.97 for two crops. The yield prediction values of wheat-maize deviated within the ranges of -3.21% to 3.47% and -4.93% to 5.88%, respectively. Based on the ensemble of RCP, precipitation was forecasted to decease by 667.40% and 261.73% in winter and summer in western as compared to eastern, respectively, which will ultimately be dropped to 105.02% and 60.87%, respectively parallel to historical. Therefore, the substantial fluctuations in precipitation caused an obvious decrease in green WF of wheat (i.e., 24.96% and 37.44%) in western and eastern, respectively. Additionally, for maize, it induced a 103.93% decrease in western and an 8.96% increase in eastern. Furthermore, increasing ETc by 8.46% and 12.45% gave rise to substantially increasing (i.e., 8.96% and 17.21%) in western for wheat-maize compared to the east, respectively. Likewise, grey wheat-maize WF findings reveals that there was an increase of 3.07% and 5.02% in western as compared to -14.51% and 12.37% in eastern. Hence, our results highly recommend the optimal use of the eastern delta to save blue-water by 16.58% and 40.25% of total requirements for wheat-maize in contrast to others. Overall, the current research framework and results derived from the adopted methodology will help in optimal planning of future water under climate change in the agricultural sector.