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Chemical fertilizer use worldwide has increased extensively last years due to expanded areas of cultivation and the need for more agricultural productivity. Increased applications of chemical fertilizers in the irrigated lands are likely to create non-point sources of chemical fertilizer species. This book presents a study of long-term modeling of the impact of the potential contamination of ground water by nitrogen, phosphorus, potassium, and sulfur chemical fertilizers and the groundwater quality for irrigation and the public water supply for the next decades. Concentrations of fertilizers ions in shallow and deep groundwater wells, under current trend in a site in Nile Valley aquifer were assessed as a case study. Groundwater Modeling System (GMS) was used to simulate 3D flow and solute transport and to predict future concentrations of agricultural chemical fertilizer species. Results of the transport simulation predict the ground water contamination at shallow depths (30 m) from chemical fertilizers usage. Protection of ground water from contamination by chemical fertilizers by best practices and other means must be applied to protect this vital resource.