The transport properties of wax and water mixtures under confinement and particularly inside catalyst nanopores is a topic of significant interest for the petrochemical industry. These mixtures are the products of the Gas-To-Liquids (GTL) process through the Fischer–Tropsch (FT) route, which experienced an increasing number of commercially viable applications over the past decades. Under reaction conditions, water is produced in high concentrations, leading to phase segregation inside the catalyst nanopores and water-assisted sintering of catalytic nanoparticles, reducing catalyst lifetime and increasing GTL operational cost. It is thus important to understand the wax–water liquid–liquid equilibrium (LLE) at reaction conditions, as it determines the maximum allowable amount of water in the FT wax. Furthermore, elucidating the phase behavior of wax–water mixture inside the nanopores, by explicit incorporation of wall effects, is essential in revealing the role of confinement on mixture phase behavior. The present study focuses on simulating the phase behavior of the n-octacosane (n-C28)–water mixture inside TiO2 nanopores. Molecular Dynamics (MD) simulations with realistic molecular models were employed, highlighting the importance of confinement on the mixture transport properties, particularly in the excess water regime. Even though phase segregated mixtures retain their structural properties compared to their bulk counterparts, significant deviations arise in terms of density profiles inside the nanopore. Water molecules organize into two discrete layers on the TiO2 surface, shielding n-C28 from the nanopore walls. Octacosane’s self-diffusion is not influenced by confinement; water on the other hand is severely hindered by the TiO2 nanopore surface, with its diffusivity bearing a strong dependence on the distance from the nanopore center.