This study is devoted to the analysis of Artificial Marine Systems (AMS) and their optimisation with emphasis on their role of mitigating anthropogenic and technological threats to the environment. Historically, AMS were created and used to enhance fishing catches, protect coastal zones and maintain biodiversity. In recent years, great strides have been made in the understanding of AMS as multifunctional tools to study, monitor and even influence the global warming processes. In fact AMS can serve as global bio-filters and controllable sinks of atmospheric carbon dioxide, in the long run mitigating global warming and enhancing sustainable preservation of marine resources. A fuzzy expert system based on the Mamdani-Sugeno modus operandi has been designed, enabling a risk/cost/benefit analysis to be performed, environmental risk to be minimised, and the optimal structure of an AMS (location, cost, size, geometrical forms, etc.) to be found. Special attention is given to the protection of the coral reef in the Eilat-Aqaba Gulf in the Red Sea.