This work aimed at investigating the effect of prolonged irrigation using low-quality water on the accumulation of Mn, Pb, and Zn in surface soils (0 – 30 cm). Two locations were selected; the first was inside El-Gabal El-Asfar farm (GAF), southeast the Nile Delta, where nine irrigation water and adjacent soil samples were collected. The second was in the middle Nile Delta (MND) region, where three water samples from Kitchener drain (mixed wastewater), Tirah drain (agricultural drainage water) and Bahr Tirah (Nile freshwater), and adjacent soil samples were collected. The total and DTPA-extractable Mn, Pb, and Zn in soils were analyzed. The soils showed total Mn below the average natural content (ANC) of the Earth's crust (900 mg kg^-1). The total Pb in four sites within GAF and all soils in MND were above the ANC (15 mg kg^-1) but below the maximum allowable concentration (MAC) of 200 mg kg^-1. Soils of GAF had total Zn contents above the ANC (70 mg kg^-1), but below the MAC (300 mg kg^-1). Mixed wastewater and agricultural drainage water-irrigated soils showed total Zn contents above the MAC. Soils of GAF showed DTPA-extractable Mn and Zn above the MAC (5 and 1.25 mg kg^-1, respectively), while Pb contents surpassed the MAC (2.0 mg kg^-1) in seven sites. The DTPA-extractable Mn and Zn in the MND soils exceeded the MAL. Soils irrigated with Kitchener drain showed available Pb double the MAC. Proper water treatments and remediation strategies are recommended to alleviate metal accumulation in the food chain.