Soybean phosphatidylcholine (SPC) and glycerol dioleate (GDO) form liquid crystal nanostructures in aqueous environments, and their mixtures can effectively encapsulate active pharmaceutical ingredients (API). When used in a subcutaneous environment, the liquid crystalline matrix gradually hydrates and degrades in the tissue whilst slowly releasing the API. Hydration dependent SPC/GDO phase behavior is complex, non-trivial, and still not fully understood. A deeper understanding of this system is important for controlling its function in drug delivery applications. The phase behavior of the mixture of SPC/GDO/water was studied as a function of hydration and lipid ratio. Small-angle X-ray scattering (SAXS) was used to identify space groups in liquid crystalline phases and to get detailed structural information on the isotropic reverse micellar phase. The reported pseudo ternary phase diagram includes eight different phases and numerous multiphase regions in a thermodynamically consistent way. For mixtures with SPC as the predominant component, the system presents a reverse hexagonal, lamellar and R3m phase. For mixtures with lower SPC concentrations, reverse cubic (Fd3m and Pm3n) as well as intermediate and isotropic micellar phases were identified. By modeling the SAXS data using a core–shell approach, the properties of the isotropic micellar phase were studied in detail as a function of concentration. Moreover, SAXS analysis of other phases revealed new structural features in relation to lipid–water interactions. The new improved ternary phase diagram offers valuable insight into the complex phase behavior of the SPC/GDO system. The detailed structural information is important for understanding what APIs can be incorporated in the liquid crystal structure.