In this numerical study, the performance of ceramic-based mullite hollow fiber (HF) membranes in a direct contact membrane distillation (DCMD) process was evaluated. Three types of membranes were tested: (i) hydrophobic membrane C8-HFM, (ii) rod-like omniphobic membrane (C8-RL/TiO₂), and (iii) flower-like omniphobic membrane (C8-FL/TiO₂). The CFD model was developed and validated with experimental results, which were performed over a 500 min period. The initial mass flux of C8-HFM was 30% and 9% higher than that of C8-FL/TiO₂ and C8-RL/TiO₂, respectively. However, the flower-like omniphobic membrane C8-FL/TiO₂ had the lowest drop in flux, around 11%, while the rod-like omniphobic membrane C8-RL/TiO₂ had a 15% reduction, both better than the 23% reduction in the hydrophobic membrane C8-HFM over the 500 min. The study also analyzed the impact of fouling by examining the variation in mass transfer coefficient (MTC) over time. The results indicated that the ceramic-based mullite HF membranes with TiO₂ flowers and rods demonstrated a high resistance to fouling compared to C8-HFM. The modified membranes could find applications in the desalination and handling of seawater samples containing organic contaminants. The CFD model’s versatility can be utilized beyond the current investigation’s scope, offering a valuable tool for efficient membrane development solutions, particularly for challenges such as the presence of organic contaminants in seawater.