Swelling of shale in clastic reservoirs poses a significant challenge, causing instability in wellbores. Utilizing water-based drilling mud with shale inhibitors is preferable for environmental reasons over oil-based mud. Ionic liquids (ILs) have garnered interest as shale inhibitors due to their customizable properties and strong electrostatic features. However, widely used imidazolium-based ILs in drilling fluids are found to be toxic, non-biodegradable, and expensive. Deep Eutectic Solvents (DES), considered a more economical and less toxic alternative to ILs, still fall short in terms of environmental sustainability. The latest advancement in this field introduces Natural Deep Eutectic Solvents (NADES), renowned for their genuine eco-friendliness. This study explores NADES formulated with citric acid (as a Hydrogen Bond Acceptor) and glycerine (as a Hydrogen Bond Donor) as additives in drilling fluids. The NADES based drilling mud was prepared according to API 13B-1 standards and their efficacy was compared with KCl, imidazolium based ionic liquid, and Choline Chloride: Urea-DES based mud. A thorough physicochemical characterization of the in-house prepared NADES is detailed. The research evaluates rheological, filtration and shale inhibition properties of the mud, demonstrating that NADES enhanced the yield point to plastic viscosity ratio (YP/PV), reduced mudcake thickness by 26%, and decreased filtrate volume by 30.1% at a 3% concentration. Notably, NADES achieved an impressive 49.14% inhibition of swelling and improved shale recovery by 86.36%. These outcomes are attributed to NADES’ ability to modify surface activity, zeta potential, and clay layer spacing which are discussed to understand the underlying mechanism. This sustainable drilling fluid promises to reshape the drilling industry by offering a non-toxic, cost-effective, and highly efficient alternative to conventional shale inhibitors, paving the way for environmentally conscious drilling practices.