This paper explores the development and optimization of artificial reefs by introducing a novel generative design method incorporating Computational Fluid Dynamics (CFD) and Optimization (BESO). Since the 1950s, efforts to create artificial reefs have been pursued to improve marine ecosystems. Our study first surveyed the existing design of artificial reefs. Addressing the limitations in existing design methods, this research employs a topological optimization strategy, focusing on optimizing space allocation for polyphony expansion within these reefs. By analyzing fluid dynamics and connecting it with an iterative optimization process, we assess the effectiveness of material exchange in these artificial structures. This is critical for the design process, considering constraints from advanced manufacturing to allow for quick production with natural-like geometries. To advance the design of artificial reefs and explore new possibilities, we introduce a novel generative design approach, where the design of the reef emerges from the interaction between CFD and BESO, through an iterative process of material removal and addition in response to the external loading condition. The artificial reef generated is compared against benchmarks of current artificial design to assess its material efficiency, structure performance, and geometrical characteristics in complex underwater conditions.