Marine biodiversity is facing increasing threats from unplanned coastal urbanization worldwide. Poor coastal planning and pollution are typically among the main factors contributing to these impacts, which affect the physiology of benthic community structuring groups, such as seaweeds. This leads to changes at both population and community levels, resulting in substantial alterations to coastal biological communities in urban areas. While some groups are severely affected, others tend to benefit from this scenario. Calcareous algae, an important foundation group for benthic communities, are among those most impacted. Conversely, ephemeral species thrive in such environments, as they are physiologically adapted to these conditions, including several green seaweed species, among other groups. These differences in performance lead to significant shifts in marine benthic community structures, typically resulting in major biodiversity losses in the affected areas. Adequate coastal planning, enhancement, management, and restoration techniques can help mitigate the loss of biodiversity in coastal urban areas. Here, we present the main causes of the problem and a summary of possible mitigation and restoration techniques.