Evaluating water quality indicators is a crucial issue in integrated water resource management, since potable water is an essential resource for the world’s health and sustainable development. The current study was developed using a coupled model of MODFLOW and MT3DMS (Mass Transport 3-Dimension Multi-Species) to integrate two water supply systems, surface water (polluted drains and canals) and ground water, to identify the contamination process of the groundwater from drains as fresh water is polluted and the contamination level exceeds the standard limits. The study was applied to two cases: the first was a hypothetical simulation and the second was the real case of the Nile Delta Aquifer (NDA). Four different scenarios were simulated to first identify groundwater contamination by total dissolved solids (TDS), and then select the more efficient protection process. The first scenario involved changing polluted drain and canal boundary conditions regarding head and concentration; the second consisted of studying the location of the polluted drain in a low permeability layer or a confined aquifer; the third was based on installing a cut-off wall in the polluted drain sides; and the fourth investigated the use of lining materials for polluted drains. The results reveal that aquifer contamination was decreased by increasing the water head of canals by 50 cm and decreasing the drain head by 50 cm and concentration by 25%, whereby large quantities of groundwater were protected. The percentages of salt repulsion in the hypothetical case were +10.66, +12.89, and +24.99%, while in NDA they were +6.29, +8.71, and +25% respectively compared with the base case. Decreasing the aquifer hydraulic conductivity led to decrease in aquifer contamination, in which the confined aquifer pollution was less than the unconfined aquifers due to the clay cap, which plays a significant role in minimizing the solute transport into the groundwater reservoir, and to reduction of the aquifer salt variation by +19.01% for the hypothetical case. The results indicate that the cut-off wall is effective for contamination management in shallow aquifers (hypothetical case) and the reduction in aquifer salt was +28.49%, whereas it had no effect in the deep aquifer (NDA), where the salt was reduced by just +0.34%. Using the drain lining scenario prevented contamination from the polluted drains and protected the freshwater in the aquifer, so that the aquifer salt mass reductions were +91.02 and +70.13% for the hypothetical case and NDA respectively, indicating that this method is more effective for controlling groundwater contamination. Polluted drains should be located in a low permeability layer to minimize the water degradation. This study represents a new contribution to groundwater protection techniques by changing the boundary conditions, installing a cut-off wall and using linings for polluted drains, and shows the way forward for the future treatment of polluted stream networks.
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