Recently, deep eutectic solvents (DESs) have received attention as extractive media for separations. In this chapter, two aspects, namely, aqueous phase separation and extractive desulfurization, are discussed. In the initial part of the chapter, the water stability of eight menthol-based DESs and two tetrabutylammonium chloride (N4444Cl)-based DESs with organic acid-based hydrogen bond donors (HBD) are discussed. The molecular dynamics (MD) simulation is here used as a tool to examine the distribution of molecules of DES and water in either phase. The intermolecular nonbonded interaction among the species of the systems was analyzed with radial distribution function, interaction energy, and hydrogen bonding analysis to understand the stability of DESs in an aqueous medium. The results show that the strong hydrogen bond plays a crucial role in the water stability of the DES. The degree of hydrogen bonding between HBD–water in terms of HBDs obtained by MD simulation can be presented in the order of acetic acid > levulinic acid > butanoic acid > pyruvic acid > hexanoic acid > octanoic acid > decanoic acid > dodecanoic acid. In the second part, noncovalent interactions are studied through the aromatic sulfur compounds (ASCs), namely, benzothiophene and dibenzothiophene with DESs. The ASCs displayed considerable and favorable free energies of solvation, indicating that oxidation will help in the crossover of these sulfur compounds from liquid fuel to a standard DES phase.