The impact of land cover/land use (LCLU) changes on surface runoff and groundwater contamination have been widely investigated, yet their impact on groundwater mixing is still poorly understood. The stress on resources in the Nile Delta triggered a vast migration of urban, agricultural, and industrial activities to its desert fringes exposing the Quaternary alluvial aquifers to contamination and introducing new sources of recharge. Here, we integrated remote sensing, chemical, and isotopic data with multivariate statistical analysis to identify groundwater sources and the mixing dynamics in response to LCLU changes. LCLU analysis indicated an increase of agricultural and urban areas from 84 km(2) to 470.5 km(2) between 1972 and 2018. These changes introduced new recharge sources including wastewater and irrigation return. Three major water sources were defined including: (1) modern precipitation (cluster 3 and Miocene aquifer; delta O-18: -4.59 to -0.47%, and delta H-2: -34.4 to 3.1%) with an estimated annual recharge of 11-13.5 x 10(6) m(2) and 5.1-6.2 x 10(6) m(2) for El-Gafra and El-Watan catchments, respectively, (2) old Nile water (subcluster 1.1; delta O-18: -0.87 to -0.53%, and delta H-2: 1 to 3.7), and (3) modern Nile water (cluster 2; delta O-18: 0.49 to 2.71%, and delta H-2: 10.5 to 24.4%). Moreover, three mixed groups were defined including: (1) a mixture of modern precipitation, wastewater and irrigation return (cluster 4; delta O-18: -1.02 to 0.37%, and delta H-2: -9.3 to 6.4%), (2) a mixture of old Nile waters and modern precipitation (subcluster 1.3; delta O-18: -1.74 to -1.38%, and delta H-2: -6.8 to -2.3%), and (3) a mixture of more than two sources with wide ranges of isotopic and chemical compositions (subclusters 1.2 and 1.4). These findings provide a good basis for further studies of groundwater mixing and assessment of contamination sources in shallow aquifers stressed by LCLU changes in hyper-arid environments.