There is a lack of methodologies that quantitatively measure the intrinsic circularity of desalination systems, particularly focusing on resource flow traceability and circular actions. This study proposes a novel framework for assessing the circular economy performance of desalination systems. By integrating a systemic indicator selection and calculation approach, this methodology enables a comprehensive evaluation of intrinsic circularity in desalination processes. The implementation and potential of the methodology are demonstrated by assessing a desalination system. The methodology enabled the identification of key hotspots, such as high energy and chemical demand, and provided insights into potential risks and benefits during the planning and analysis phases. The system showed a 94% circular water inflow and a 91.2% circular water outflow. The system also achieved an 85.9% water recovery rate. Hotspots were identified in energy and chemical usage, highlighting areas for potential optimisation. A scenario analysis further revealed that the methodology is capable of capturing changes in the system, offering a detailed understanding of the resource recovery process. Moreover, it shows the methodology can be applied to different desalination schemes (e.g. Minimal Liquid Discharge, Conventional and Zero Liquid Discharge). The current research advances the planning and strategic implementation of circular strategies in desalination, emphasising the importance of intrinsic circularity in achieving sustainable water management solutions. The findings contribute to the development of innovative methodologies for enhancing the sustainability of desalination systems.