Coral reefs are vital ecosystems facing rapid degradation. This research explores architectural design solutions for bio-enhancing modular prototypes to support coral attachment and growth. Inspired by coral polyps, nine biomimetic designs were created using Maya and Rhinoceros 3D to optimise surfaces for coral settlement. A total of 75 prototypes (15 × 15 cm) were fabricated, incorporating four materials—PETG, concrete, oyster concrete, and clay—and seven colour variations—sand, translucent green, translucent brown, red, pink, grey, and reddish. The findings indicate that 3D printing with PETG was the most efficient fabrication method but required structural support and long-term underwater testing, while oyster concrete demonstrated potential for self-sustaining structures. This study highlights the role of architectural design in marine restoration, promoting biodiversity and resource-efficient solutions. By integrating corals into the design, these structures can self-grow and adapt, reducing material consumption and long-term maintenance.