A strategic instrument for the sustainable conservation of the fragile marine ecosystem is the designation of Marine Protected Areas (MPAs), within which various regulations exist for the protection of highly vulnerable species and habitats. These regulations can be depicted on Electronic Navigational Charts (ENCs) based on the new International Hydrographic Organization (IHO) S-100 series of standards, which support Marine Information Overlays (MIOs) that enrich the portrayed information by including both static and dynamic information, such as vessels traffic, tides, currents, and weather conditions, as well as essential information for the regulation of MPAs. Although, the new IHO S-122 Product Specification introduced specifically for the MPAs has been developed to encapsulate geospatial information for these regulations, the present edition does not specify portrayal. This paper reviews the legal foundation for the protection of marine mammals as well as the mapping methods used in selected study cases and builds upon these to present new, intuitive portrayal symbols for depicting the type of MPAs in combination with the regulations to be enforced on ENCs. Moreover, to support the global efforts for the protection of marine biodiversity, contemporary navigation systems aboard vessels can be used to enforce environmental regulations, and operations centers ashore can also monitor vessels’ passage and activities in MPAs. In that respect, this paper also discusses the concepts of Ecosystem Protection Zones and Environmental Risk Contours that can facilitate environmental risk-based voyage planning and preventive alarm services through Electronic Chart Display and Information Systems (ECDIS).