The current work aimed at verifying the modifications in chemical, physical, fertility, and environmental quality of alluvial soils southeast of the Nile Delta of Egypt following 25-years irrigation using two marginal water sources; agricultural drainage water (ADW) and sewage effluent water (SEW). Two sites irrigated with ADW and SEW were chosen and compared with a nearby site irrigated with the Nile freshwater. At each site, ten samples of irrigation water and adjacent (around 50 m) topsoil (0 – 30 cm) were collected and analyzed. Marginal water irrigation caused slight changes in soil properties. The soil chemical quality index was adversely affected through increasing the pH, electrical conductivity, and exchangeable sodium percentage. Available micro-nutrients (Fe, Mn, Zn, and Cu) and P in SEW-irrigated soils were increased. The physical quality index was also increased, but mainly due to inherent soil properties (particle size distribution) rather than irrigation water. Parent materials governed soil total contents of Cr, Co and Ni, while contents of Cd, Cu, Pb, and Zn were closely related to irrigation water. The environmental quality index showed increasing trend in the ADW-irrigated soils, while a decrease in the SEW-irrigated soils. The marginal water irrigation resulted in positive changes in soil quality index exhibiting increases of 14 and 21 % in the ADW- and SEW-irrigated soils over the Nile freshwater-irrigated soils, respectively. It is recommended to perform periodic monitoring for irrigation water and soil quality in the studied area. Proper in-situ remediation scenarios and on-farm practices should be considered in future management.