Artificial reefs (ARs) are pivotal underwater structures designed to protect marine ecosystems and enhance fishery resources; however, quantifying their functional benefits, such as wake and upwelling effects, remains challenging due to the complexity of hierarchical hydrodynamic interactions. This study evaluates the hydrodynamic performance of six different AR set configurations—categorized into three idealized models (Hexa, Rect, and Pyra) and three practical models reflecting field placement (Tri, Tetra, and Penta)—using an element-based finite volume method with ANSYS-CFX. Each set comprised 100 cube-type AR units to satisfy the South Korean regulation requiring a minimum facility volume of 800 m³. The numerical results demonstrated significant variations in wake area (WA) and upwelling area (UA) across the configurations, revealing that WA was predominantly developed near the seabed due to structural resistance, while UA reached its peak near the top of the structures before diffusing upward. Notably, the practical models (Tri, Tetra, and Penta) exhibited superior performance compared to idealized models, as their higher geometric complexity effectively induced flow separation and vertical deflection, resulting in more extensive WA and UA despite having relatively lower heights. From an ecological perspective, the extensive WA in practical models provides optimal habitats for Type A (demersal) fish, while the robust upwelling flows support Type B (reef-associated) and Type C (migratory) species by enhancing nutrient transport to the upper water column. These findings suggest that radial, scattered placement strategies are more effective for multi-species resource enhancement than simple dense stacking, providing essential quantitative data for establishing scientific guidelines for the strategic placement of artificial reefs.