The Masjed-e-Soleyman dam, situated in southern Iran, is a rock-fill dam with a clay core, reaching a height of 178 meters. During the construction and impounding phases, notable pore water pressure was developed within the core. The dissipation rate of this pressure is considerably slow, persisting long after impounding. Nonetheless, progressive deformations and irregularities have been observed and documented on the surface of the dam's body, with no significant decrease in the rate of deformation. These deformations have raised concerns regarding the safety and stability of the superstructure. This study aims to investigate all factors influencing such deformation behavior by analyzing instrumental data and employing a mechanical-fluid three-dimensional numerical model. A modified softening-hardening constitutive model is utilized to simulate the phenomena of rock-fill particle crushing and saturated collapse within the upstream rock-fill shell materials. Additionally, a viscoelastic creep model is employed to simulate creep deformations. Subsequently, a robust hypothesis concerning the long-term mechanism of dam deformation behavior is formulated. According to this hypothesis, the main contributors to the complex behavior of this dam are the creep deformations of the rock-fill shell and the clay core's deformation under constant volume conditions.