Seawater reverse osmosis (SWRO) is the leading technology for large-scale desalination, yet membrane fouling remains a major limitation affecting performance stability, energy consumption, and membrane lifespan. Conventional fouling monitoring in SWRO plants relies primarily on hydraulic indicators such as pressure drop and flux decline, which often detect fouling only after it has reached an advanced stage. This study proposes an advanced fouling assessment approach based on permeate quality degradation indicators, shifting permeate quality from a passive compliance parameter to an active diagnostic signal. Long-term operational data from full-scale SWRO plants were analyzed to investigate the temporal evolution of permeate conductivity, salt passage, and their relationship with hydraulic performance and cleaning-in-place (CIP) events. The results show that permeate quality degradation evolves progressively during fouling development, frequently preceding significant hydraulic deterioration, and responds rapidly and reversibly to CIP operations. Clear evidence of decoupled behavior between permeate quality and pressure drop was observed, highlighting the early-warning potential of permeate quality indicators. The findings demonstrate that permeate quality degradation provides a sensitive, robust, and operationally practical indicator of membrane fouling severity and dynamics. Integrating these indicators into routine SWRO monitoring frameworks can enhance fouling diagnosis, optimize cleaning strategies, and support the development of advanced, data-driven control and predictive maintenance systems for desalination plants.