Shipwreck sites are open systems, allowing the exchange of material and energy across system boundaries. Physical processes dominate site formation at fully submerged wreck sites, and in turn influence chemical and biological processes at many stages of site formation. Scouring presents a fundamental yet poorly understood threat to wreck sites, and the processes and patterns of erosion and deposition of sediments and artefacts at wreck sites are poorly understood. Laboratory and field-based experiments to study these phenomena are time-consuming and expensive. In this study, open-source computational fluid dynamic (CFD) simulations are used to model the processes and patterns of flow, erosion, and deposition at fully submerged wreck sites. Simulations successfully capture changes in the flow regime in the environment of the wreck as a function of incidence angle, including flow contraction, the generation of horseshoe vortices in front of the wreck, the formation of lee-wake vortices behind the structure, and increased turbulence and shear stress in the lee of the wreck site. CFD simulations demonstrate that horseshoe vortices control scour on the upstream face of structure but play a minimal role in scouring on the lee side. Lee-wake vortices dominate behind the structure, with low-pressure zones in the lee of the wreck capturing flow. The amplification and reduction of wall shear stress and turbulent kinetic energy in the lee of the vessel form distinctive patterns in relation to flow direction, with areas of amplified and reduced wall shear stress and turbulent kinetic energy demonstrating excellent spatial correlation with erosional and depositional patterns developed at real-world wreck sites.