This research focuses on the implementation of the Building with Nature (BwN) approach in the design of artificial coral reefs. The goal is to explore environmental preferences and design tools for coral development, considering both coral habitat potential and coastal protection services. The research also aims to optimize artificial reef design for a case study in Addu City, Maldives. A conceptual model is developed based on an extensive literature review, incorporating critical engineering and ecological variables relevant to coral habitat potential and coastal protection services. This conceptual model serves as a practical design tool, fulfilling three primary purposes: identifying variables that require further examination to explore coral habitat potential, identifying variables that require analysis to explore coastal protection services, and identifying design variables that influence physical-chemical and biological variables for potential integral solutions. The research also utilizes OpenFOAM, a numerical modeling tool commonly used in coastal engineering, to design artificial reefs. OpenFOAM accurately models flow and turbulence regimes, crucial for the ecological and biological functioning of coral reefs. An OpenFOAM numerical model is set up, calibrated, and validated for the case study in Addu City. Three design alternatives with different slopes are evaluated using a multi-criteria analysis (MCA), considering criteria such as coastal protection, coral habitat potential, and costs. The numerical model is applied to assess flow regimes and wave transmission for different design variables. Based on the MCA results and the evaluation of criteria, an artificial reef with a mild slope of 1:3 is selected as the optimal integral solution for the case study. This design performs well in terms of coastal protection, coral habitat potential, and costs. The research demonstrates that the conceptual model and OpenFOAM numerical model are valuable design tools for assessing and optimizing artificial reef design, adhering to the principles of the BwN approach. In conclusion, this research contributes to expanding knowledge and developing tools for implementing the BwN approach in artificial reef design. By considering both coral habitat potential and coastal protection services, the design of artificial reefs can be optimized to provide multiple benefits, including environmental and socio-economic values. The conceptual model and numerical modeling tool offer practical assistance in the design process, promoting the integration of nature and engineering for sustainable coastal solutions.