Coastal engineering works, especially the outer breakwaters of ports where environmental conditions are usually good, often constitute new habitats for marine littoral species. Their potential indirect contribution to the regeneration and conservation of protected species opens up a new perspective in protection of marine biodiversity. This is particularly true when these works harbour, as we show here, important reproductive populations of species that are threatened or even in danger of extinction. We provide integrated data on protected marine species in Southern Iberia established on different substrata (quarried dolomitic rocks, concrete cubic blocks, concrete tetrapods and vertical concrete walls) that are used in the construction of artificial levees that could potentially be Artificial Marine Micro-Reserves (AMMRs). We also present the first evidence of the ‘reserve effect’ in potential AMMRs and we discuss the need for the creation of AMMRs including their effective networking (AMMRNs), supporting data for which has been observed by studying coastal facilities subjected to strict access restrictions (for security reasons, not conservation). These facilities have acted as valuable proxies and, in reality, potentially act as AMMRs, as well as having a role in helping to detect and control invasive species. We discuss the ecological engineering aspects related to the design and type of materials used in coastal constructions with a view to aiding the integration of these into existing coastal ecosystems as well as promoting greater settlement of species and therefore increases in biodiversity. Finally, the environmental implications of AMMRNs within the future implementation strategy of the Water Framework Directive 2000/60 EC are also discussed.