Lack of active sorption sites in sandy soils renders metals added by irrigation water more labile and increases their soil-to-plant transfer. Thus, this study investigated the long-term impacts of irrigation using sewage effluents and contaminated groundwater on metal accumulations in TypicTorripsamment soils, and edible parts of food crops. Nine sites in El-Gabal El-Asfar farm, south-eastern to the Nile Delta of Egypt, were selected. At each site, irrigation water, soil (0–30 cm), and the crop’s edible part were sampled in triplicates and analyzed for Mn, Pb, and Zn. Results revealed significant (p < 0.05) differences in metal concentrations among water sources. Thus, constant irrigation caused significant spatial variations in total and available metal contents in soils. Total contents of Pb (in four sites) and Zn (in all sites) exceed the lithosphere range, while the available contents of the three metals exceeded the safe limits in all soils. The index of geo-accumulation indicated no Mn pollution but showed elevated pollution risks for Pb and Zn. The three metals showed high availability ratios, proving the effect of light soil texture. The multivariate statistical analysis indicated that Mn and Zn had similar geochemical behaviors in soils. Metal contents in all crop’s edible parts surpassed the safe limits. The bioaccumulation factor (BAF) was less than 1.0 for Mn and Zn but higher than 1.0 for Pb. The highest BAFs occurred in cabbage leaves, indicating the phytoextraction potential of this species. Sufficient water treatment and proper remediation techniques are recommended to alleviate metal accumulation in food crops and their transfer via the food chain.