Background: Coastal landscapes are being transformed as a consequence of the increasing demand for infrastructures to sustain residential, commercial and tourist activities. Thus, intertidal and shallow marine habitats are largely being replaced by a variety of artificial substrata (e.g. breakwaters, seawalls, jetties). Understanding the ecological functioning of these artificial habitats is key to planning their design and management, in order to minimise their impacts and to improve their potential to contribute to marine biodiversity and ecosystem functioning. Nonetheless, little effort has been made to assess the role of human disturbances in shaping the structure of assemblages on marine artificial infrastructures. We tested the hypothesis that some negative impacts associated with the expansion of opportunistic and invasive species on urban infrastructures can be related to the severe human disturbances that are typical of these environments, such as those from maintenance and renovation works. Methodology/Principal Findings: Maintenance caused a marked decrease in the cover of dominant space occupiers, such as mussels and oysters, and a significant enhancement of opportunistic and invasive forms, such as biofilm and macroalgae. These effects were particularly pronounced on sheltered substrata compared to exposed substrata. Experimental application of the disturbance in winter reduced the magnitude of the impacts compared to application in spring or summer. We use these results to identify possible management strategies to inform the improvement of the ecological value of artificial marine infrastructures. Conclusions/Significance: We demonstrate that some of the impacts of globally expanding marine urban infrastructures, such as those related to the spread of opportunistic, and invasive species could be mitigated through ecologically-driven planning and management of long-term maintenance of these structures. Impact mitigation is a possible outcome of policies that consider the ecological features of built infrastructures and the fundamental value of controlling biodiversity in marine urban systems.