Molecularly Imprinted Polymers (MIPs) are traditionally synthesized in organic solvents, resulting in poor compatibility with water and poor molecular recognition of targets in aqueous environments; Therefore, developing a green process to synthesize such MIPs would make the process more sustainable and production more environmentally friendly. To achieve these goals, a new hydrophilic molecularly imprinted resin (DES-HMIR) based on a deep eutectic solvent in water with excellent selective molecular recognition in the aqueous phase was synthesized; thus the process avoids the consumption of large amounts of organic solvents. During the synthesis, DES was used simultaneously as a porogen and cosolvent for the template in order to improve the imprinting factor and increase the specific surface area of the DES-HMIR. Due to its specific recognition performance and water phase compatibility, DES-HMIR can specifically recognize and extract targets from aqueous matrices. The DES-HMIR obtained showed excellent specificity for the analytes compared to commercial adsorbents such as HLB, C18, silica and SCX. The DES-HMIR could be easily regenerated with only 0.1 mL 50% acetonitrile water at room temperature and reused 26 times without a significant decrease in the adsorption capacity at pH 7. DES-HMIR demonstrated excellent and specific recognition properties for its target molecules in aqueous matrices, enabling their use in a variety of promising applications including environmental, biological and clinical applications. Finally, the synthetic strategy proposed in this thesis offers a simple, efficient and environmentally friendly protocol for the preparation of water-compatible MIPs.