The Quaternary coastal plain aquifer down gradient of the Wadi Watir catchment is the main source of potable groundwater in the arid region of south Sinai, Egypt. The scarcity of rainfall over the last decade, combined with high groundwater pumping rates, have resulted in water-quality degradation in the main well field and in wells along the coast. Understanding the sources of groundwater salinization and amount of average annual recharge is critical for developing sustainable groundwater management strategies for the long-term prevention of groundwater quality deterioration. A combination of geochemistry, conservative ions (Cl and Br), and isotopic tracers (87/86Sr, δ81Br, δ37Cl), in conjunction with groundwater modeling, is an effective method to assess and manage groundwater resources in the Wadi Watir delta aquifers. High groundwater salinity, including high Cl and Br concentrations, is recorded inland in the deep drilled wells located in the main well field and in wells along the coast. The range of Cl/Br ratios for shallow and deep groundwaters in the delta (∼50–97) fall between the end member values of the recharge water that comes from the up gradient watershed, and evaporated seawater of marine origin, which is significantly different than the ratio in modern seawater (228). The 87/86Sr and δ81Br isotopic values were higher in the recharge water (0.70,723 < 87/86Sr < 0.70,894, +0.94 < δ81Br < +1.28‰), and lower in the deep groundwater (0.70,698 < 87/86Sr < 0.70,705, +0.22‰ < δ81Br < +0.41‰). The δ37Cl isotopic values were lower in the recharge water (−0.48 < δ37Cl < −0.06‰) and higher in the deep groundwater (−0.01 < δ37Cl < +0.22‰). The isotopic values of strontium, chloride, and bromide in groundwater from the Wadi Watir delta aquifers indicate that the main groundwater recharge source comes from the up gradient catchment along the main stream channel entering the delta. The solute-weighted mass balance mixing models show that groundwater in the main well field contains 4–10% deep saline groundwater, and groundwater in some wells along the coast contain 2–6% seawater and 18–29% deep saline groundwater.A three-dimensional, variable-density, flow-and-transport SEAWAT model was developed using groundwater isotopes (87Sr/86Sr, δ37Cl and δ81Br) and calibrated using historical records of groundwater level and salinity. δ18O was used to normalize the evaporative effect on shallow groundwater salinity for model calibration. The model shows how groundwater salinity and hydrologic data can be used in SEAWAT to understand recharge mechanisms, estimate groundwater recharge rates, and simulate the upwelling of deep saline groundwater and seawater intrusion. The model indicates that most of the groundwater recharge occurs near the outlet of the main channel. Average annual recharge to delta alluvial aquifers for 1982 to 2009 is estimated to be 2.16 × 106 m3/yr. The main factors that control groundwater salinity are overpumping and recharge availability.