Saltwater intrusion (SWI) is a type of pollution that adversely affects the quality of groundwater in coastal aquifers. The Nile Delta aquifer (NDA) in Egypt contains a large amount of freshwater. Increasing abstraction from the aquifer and sea level rise have led to an increase in SWI, which has reached up to 100 km inland. Therefore, practical measures are required to prevent further SWI. This study aims to identify an optimal well system to manage the intrusion of saline water in NDA using a number of management systems, including pumping of brackish water, aquifer recharge, and abstraction of the freshwater. SEAWAT code is used to simulate SWI in the aquifer considering different scenarios of pumping and sea level rise. Four scenarios are used to control SWI, including: decreasing pumping from the aquifer, increasing recharge using treated waste water, increasing abstraction of brackish water for desalination, and a combination of these systems. The results showed that increasing recharge could lead to greater retardation of SWI (19.5%) than decreasing pumping (6.2%) and abstraction of brackish water (5.9%). However, a combined well system of pumping, recharge and abstraction is shown to be a more effective tool to control SWI in coastal aquifers, with retardation percentage of 21.3%.