Strongly concentrated agriculture along the River Nile in Egypt, combined with hydrologic changes related to the construction of the Aswan High Dam in the 1970's, has led to increasing salinization and waterlogging of agricultural areas. Successful control and remediation of these problems requires accurate understanding of the shallow Quaternary aquifers within the Nile Valley. While extensive conceptual models have been developed by the Egyptian RIGW, published numerical models have yet to incorporate all features of the conceptual model. In particular, marine affinity of some shallow groundwaters within the valley (Cl −as the predominant anion) indicates significant leakage from deeper Cretaceous aquifers into the shallow Quaternary aquifers, a feature that is not present in current models. In this study, groundwater profile modeling incorporating the bedrock leakage demonstrates that its shallow appearance requires hydraulic separation of surficial from deep-recharged zones of the Quaternary aquifer. This separation occurs near the boundary between reclaimed and traditional agricultural lands, which is also the primary site of waterlogging. Apparently, excessive recharge presumed to occur beneath the reclaimed lands does not penetrate deeply, and therefore might be easily remediated with shallow drains. Profound similarities exist between the Nile Valley salinization cases and the occurrence of shallow ‘nuisance water’ in desert southwestern U.S. cities (e.g. Las Vegas). The U.S. experience with this problem may provide useful guidance in addressing Nile Valley salinization and waterlogging issues in the future. In general, irrigation-related recharge from the reclaimed lands in the Nile Valley may have a much more localized impact on traditional lands than previously thought.