We developed the first fully automated rotating disk extraction system with flow control that uses hydrophobic natural deep eutectic solvents to preconcentrate polycyclic aromatic hydrocarbons from drinking water. The core innovation lies in the seamless combination of a porous polyetherimide disk, pre-coated with a thymol/carvone natural deep eutectic solvents layer, with an automated dynamic flow platform, uniting the advantages of rapid mass transfer via disk rotation and the precision, reproducibility, and scalability of flow-based automation. Systematic optimization of key operational parameters, including rotation speed, sample flow rate, extraction time, and eluent volume, enabled highly efficient analyte capture and release, achieving enrichment factors up to 6 in static mode, with detection limits as low as 0.1-6.9 μg L-1. The automated setup demonstrated high analytical performance, delivering intra-day and inter-day precision (RSD ≤6.4 % and ≤12 %, respectively) and recovery rates of 85-114 % across diverse real-world matrices, including tap water, bottled water, and black tea infusions. Beyond experimental validation, all-atom classical molecular dynamics simulations provided mechanistic insight, revealing strong π-π interactions between analytes and thymol that drive efficient phase transfer within the NADES layer. Environmental sustainability was quantitatively assessed using the AGREEprep metric, yielding a favorable score of 0.71, largely due to the substitution of hazardous solvents with green NADES and the minimized solvent footprint enabled by automation. Overall, this study delivers a robust, automated, and environmentally responsible platform, establishing a new method for liquid-phase microextraction that integrates automation and green chemistry. This platform offers broad potential for sensitive, scalable monitoring of environmental, food, and industrial samples.
