Summary1. Coastal landscapes are being transformed as a consequence of the increasing demand for urban infrastructure to sustain commercial, residential and tourist activities. A variety of man-made structures, such as breakwaters, jetties and seawalls have thus become ubiquitous features of intertidal and shallow subtidal habitats. This transformation will accelerate in response to the exponential growth of human populations and to global changes, such as sea-level rise and increased frequency of extreme meteorological events (e.g. storms). Here, we provide a critical overview of the major ecological effects of increasing infrastructure to marine habitats, we identify future research directions for advancing our understanding of marine urban ecosystems and we highlight how alternative management options might mitigate their impacts. 2. Urban infrastructure supports different epibiota and associated assemblages and does not function as surrogate of natural rocky habitats. Its introduction in the intertidal zone or in nearshore waters can cause fragmentation and loss of natural habitats. Furthermore, the provision of novel habitat (hard substrata) along sedimentary shores can alter local and regional biodiversity by modifying natural patterns of dispersal of species, or by facilitating the establishment and spread of exotic species. 3. Attempts to use ecological criteria to solve problems of urban infrastructure are promising. Incorporating natural elements of habitat (e.g. wetland vegetation; seagrass) into shoreline stabilization can reduce ecological impacts, without impinging on its efficacy in halting erosion. Likewise, improving the ecological value of artificial structures by adding features of habitat that are generally missing from such structures (e.g. rock-pools) can contribute to mitigation of the detrimental effects of urbanization on biodiversity. Management of anthropogenic disturbances (e.g. maintenance works; harvesting) to artificial habitat is, however, necessary if such attempts are to be successful. 4. Synthesis and applications. Increasing our understanding of the ecological functioning of marine habitats created by urban infrastructure and incorporating ecological criteria into coastal engineering are crucial for preserving biodiversity in the face of the growth of human populations in coastal areas and of forecasted global changes. Achieving this goal will need strong collaboration between engineers, managers and ecologists.