In case of poor-quality oil refining in the oil pipeline, water accumulations are formed, increasing hydraulic losses during transportation and contributing to corrosion processes. Hydrodynamic cleaning, which uses pumped oil flow, has been investigated due to its cost-effectiveness and adaptability for pipelines of varying diameters. This study develops a finite element hydrodynamic model to simulate the removal of water accumulations from inclined pipelines (inclination angle α = 45°). The model reveals a clear relationship between inlet velocity and Multiphase flow patterns, demonstrating transitions from stratified flow (ST) at velocities below 0.1 m/s, to stratified with mixing (ST&MI) at 0.1–0.2 m/s, and finally to a dispersed water-in-oil (DW/O) pattern beyond 0.2 m/s. These velocity transitions are achieved in controlled steps: a steady increase to 0.1 m/s within 20 seconds, followed by acceleration phases reaching 0.25 m/s by 100 seconds. The DW/O regime exhibits the highest cleaning efficiency, reducing water volume from 660 ml to 273.29 ml over 125 seconds—a 58.5% reduction. The analysis further shows an initial rise in pressure gradient within the ST regime, peaking during the first plateau (0.1 m/s) before stabilizing and significantly declining in the DW/O regime at velocities exceeding 0.25 m/s. These findings emphasize the importance of optimizing flow velocity to achieve effective water removal while minimizing hydraulic losses. The study also highlights limitations in existing experimental setups, which predominantly use small diameters (<50 mm), and underscores the need for larger-scale experiments to validate these findings in real-world pipeline operations.