Safe drinking water remains an issue all around the world, especially in arid countries that require seawater desalination to obtain safe water. This research seeks to analyze water quality at the major stages of an SWRO plant, i.e., raw seawater intake, RO permeate, reject brine, and distribution network water. For the study, conventional physicochemical methods of water quality analysis, as well as electrochemical impedance spectroscopy, were used. Four water samples were taken at different stages of the treatment process: raw seawater (feed water), RO permeate, reject brine, and distribution network water. Physicochemical parameters, such as pH, electrical conductivity, total dissolved solids (TDS), major ions (Na⁺, Cl⁻, Ca²⁺, and Mg²⁺), and heavy metals (Zn, Cu, Cr, and Hg) concentrations, were evaluated. Electrochemical impedance spectroscopy was used to investigate ionic transport, dielectric relaxation, and interfacial polarization mechanisms within the tested solutions. It has been shown that RO membranes are capable of rejecting major ions up to 95–99%, as can be seen in the low values of conductivity and TDS of RO permeate. EIS analysis also allowed for identifying specific electrochemical characteristics of all four types of water, with brine being characterized by the highest polarization rates and relaxation times.