The presence of uplift pressures in cracked plain concrete hydraulic structures is a major concern for their durability, serviceability and stability. To assess the performance of cracked structures several mechanical and hydraulic response parameters must be computed. This paper presents the development, implementation and application of a new nonlinear combined segregated fully-coupled hydromechanical model for application to non-planar 3D hydraulic fractures where complex flow is occurring. The eXtended Finite Element Method (XFEM) formulation is used, as it facilitates the computation of the crack aperture as well as the application of water pressure on crack surfaces for the simulation of hydraulic fracture initiation and propagation. To take into consideration the effects of drainage in numerical modeling and simulation, two coupled (multi-physics) finite element models are used; (1) one for the uplift pressures where a hydraulic mesh with refinement around drains is used, and (2) one for the mechanical response coupled with the computation of the unsaturated interstitial seepage problem. The two subproblems are solved using a partitioned procedure, as they have different resolution requirements. Finally, the mechanical mesh and the hydraulic mesh have non-matching discrete interfaces that must be coupled while respecting the equilibrium of the applied loads. Applications of the proposed hydromechanical constitutive model and numerical solution strategy to different problems are presented on a wedge splitting test and a full scale gravity dam including multiple drainage configurations. A case study adapted from a real dam is also given with a complex 3D non-planar discontinuity surface.