In addition to enduring severe environmental conditions and strong seismic activity, the design of an offshore substation located in the Taiwan Strait must address the technical challenge of scour formation induced by waves and currents. Scour phenomena can occur shortly after the installation of the offshore substation and can persist throughout the operational lifespan of a project if an appropriate scour protection system is not in place. This study focuses on the adverse impacts of scour phenomena and presents an approach to account for scour effects in the design of the substructure and foundation for an offshore substation. It was found that scour can significantly affect pile capacities, the dynamic responses and fatigue lifetime of the substructure, either necessitating larger pile dimensions and heavier steel substructures or a substantial periodic inspection and maintenance schedule. However, scour protection systems are not always cost-effective, depending on site-specific conditions. Therefore, it is essential to consider scour protection strategies at the beginning of the project to fully understand all constraints and optimize the total project cost.