Human activities contribute numerous hydrogeological threats including waterlogging, soil salinization and water pollution in East Nile Delta region. Landsat Thematic Images were utilized to detect the environmental changes in the study area during the last three decades. Remote sensing and Geographic Information Systems data were integrated to monitor and measure surface areas of agricultural and urban developments. Risk assessment maps were constructed for waterlogging and soil salinization threats. The results cleared that both evaporation from logged and flood irrigation water surfaces cause up to 30% of water loss. The logged areas increased from 25km2 in 1984 to 180km2 in 2014 along the El-Tina plain which represents the most threated zone. The total changes of waterlogging cover at east Nile Delta varies between 930km2 in 1989, 685km2 in 1998 after the construction of El-Salam Canal and 1044km2 in 2014. The total estimated water loss by direct evaporation was up to 23.6Mm3/year. Following the construction of El-Salam Canal in 1998, water and drainage effluents into Manzala Lake were decreased creating shrinkage in its surface area by 45%. Consequently, water quality of Manzala Lake was severely deteriorated due to the throwing of municipal and irrigational sewages.