Water scarcity in Tunisia’s semi-arid regions necessitates advanced brackish water desalination solutions. This study evaluates the long-term performance and fouling characteristics of the largest brackish water reverse osmosis desalination plant in southern Tunisia over a period of 5026 days. The plant employs two-stage spiral-wound membrane elements to treat groundwater with a salinity of 3.2 g L−1. The pre-treatment process includes oxidation, sand filtration, and cartridge filtration, along with polyphosphonate antiscalant dosing. Membrane performance was assessed through the analysis of operational data, standardization of permeate flow (Qps) and salt passage (SPs), and the calculation of water (A), solute (B), and ionic (Bj) permeability coefficients. Over the operational period, there was an increase in operating pressure, pressure drop, and permeate conductivity, accompanied by a gradual increase in SPs as well as in the solute B and ionic Bj permeability coefficients. The average B increased by 82%, reflecting a decrease in solute rejection over time. Additionally, the ionic permeability coefficients for both SO42− and Cl− ions increased, with Cl− showing an 88% increase and SO42− showing an 87% increase. The produced water’s salinity increased by 67%, indicating a significant loss of membrane performance. To identify the cause of these problems, membrane characterization was analyzed using visual inspection, X-ray fluorescence (XRF), and Fourier transform infrared spectroscopy (FTIR). The characterization revealed the complex nature of the foulants, with a predominant presence of calcium sulfate, along with minor quantities of calcite, dolomite, and silica. The extent of CaSO4 deposition suggests poor antiscaling efficiency, highlighting the critical importance of selecting an effective antiscalant to mitigate membrane fouling.