This paper discusses the effects of the free surface and the propeller on a benchmark Post-Panamax Ship, Duisburg Test Case (DTC). The experimental results are already available in the literature. The computational study carried out in this work is verified first with the experiments and then used to explain some of the physical aspects associated with viscous ship flows. There are two interesting outcomes of this work. The first one is, the existence of the propeller contributes to the pressure resistance of the ship by increasing the wave elevations along the hull and the fluid domain substantially. The second outcome is; by changing the pressure distribution along the hull and the propeller, the free surface increases the efficiency of the propulsion system. These specific outcomes are thoroughly discussed in the paper with CFD generated results and physical explanations.