In this work, the performance of a Reverse Osmosis (RO) process using different types of reverse osmosis (RO) and nanofiltration (NF) membranes is evaluated for brackish water desalination for producing irrigation-grade water. The proposed desalination system is a single-stage system, where three types of RO and two NF membranes were examined. The different desalination systems were simulated using ROSA72 software. In order to validate the theoretical model, the results obtained from the simulation were compared to those obtained from the experiment conducted in this work. The El-Moghra aquifer of Egypt is considered the test bed due to a considerable amount of data being available for this aquifer. The El-Moghra aquifer has 79 wells, and the available water data, when checked against several quality parameters, show that none of the investigated wells are suitable for direct irrigation without treatment due to problems of salinity, the sodium adsorption ratio, and low water quality according to the irrigation water quality index values. The obtained results show that nanofiltration membranes exhibited superior energy efficiency compared to reverse osmosis membranes. However, what sets the nanofiltration membranes apart is their ability to elevate water quality in 89.9% of the total investigated wells to an acceptable level for agricultural purposes. This underscores the nanofiltration membranes as a highly effective alternative to reverse osmosis membranes, demonstrating the capability to produce water suitable for irrigation while concurrently reducing operational costs due to the lower energy consumption in nanofiltration-based systems.