Modern analytical chemistry techniques meet the need for greater attention to ecological and economic aspects. It is becoming necessary to seek solutions to reduce harmful waste production, especially in large quantities. High-performance liquid chromatography is a technique widely used in many industries, including mainly pharmaceuticals, and requires an approach to reduce the significant amount of organic solvent waste. One of the green chemistry solutions is using environmentally benign substitutes, such as pure water, supercritical dioxide, and ethanol. Our work focuses on the preparation and application of new stationary phases with embedded hydrophilic groups for separations using pure water in liquid chromatography. Polar-embedded stationary phases are obtained by attaching a phosphodiester group and 4 different hydrophobic molecules. The studies consisted of hydrophobicity measurements, concentration dependence of retention of the organic additive to the mobile phase, and chromatographic separations of polar and non-polar substance mixtures in RP-LC and HILIC systems. Three mixtures were studied: purine alkaloids, benzene, and polycyclic aromatic hydrocarbons and nucleosides. The stationary phases interact differently with the analytes depending on the attached hydrophobic group. It is possible to use pure water to separate each mixture under study. It is also significant that it has been possible to separate a mixture of completely non-polar compounds using pure water for the first time. The research being carried out is crucial in synthesizing new polar-embedded stationary phases, providing work versatility and high environmental performance.