A proper assessment of maritime security risks at the national level is crucial to a national maritime security plan (NMSP) in order to secure the concerned country’s ports, vessels and territorial sea. Thus, the importance of implementing a national maritime security assessment (NMSA) to counter security threats and ensure the continuity of national and international trade. The most important set of international regulations concerning maritime security is the International Ship and Port Facility Security (ISPS) Code, which includes revision, approval and control of compliance of the Port Facility Security Plan (PFSP), which shall be based upon the Port Facility Security Assessment (PFSA). This paper proposes a mathematical dynamic model that calculates in real time the residual risk for the whole country and each of its ports by adapting and expanding the formula and procedures established in the Code, which since it has already been implemented around the world, gives the opportunity to take advantage of this quantitative solution to administrate maritime security risks on a nation-wide basis and create an effective national maritime security plan, which would allow the concerned authorities to improve situational awareness and adapt to security changes through a better planning of human, economic and material resources to deter security threats. The model was tested with the use of five encoded categories as countries, each of them with three ports, which encompassed three port facilities. The results indicate that this methodology is easy to implement and widespread use of that model could strength robustness in national security.