Urbanization has negative consequences for the integrity of ecosystems and services they provide, by reducing their extent and quality in both aquatic and terrestrial environments. Few studies have explored how urban infrastructure expansion affects the spatial connectivity of coastal ecosystems by provoking their fragmentation and loss. Here we explore changes in the spatial connectivity of coastal ecosystems due to urbanization, analyzing ecosystem extent and concatenation with urban infrastructures (shared perimeter) in four bays of the Coquimbo region of northern Chile (from 29°S to 32°S) as model systems. Increase in natural-to-urban concatenation patterns were observed in most urbanized bays; sandy beaches and wetlands were the habitats most connected with urban infrastructures like roads and coastal artificial defenses. Availability of ecosystem services is compromised by progressive loss of natural connectivity and poor governance structure, which seems to confer high vulnerability to urbanized bays with future urban expansion. Complementary actions are proposed to reduce the vulnerability of coastal urban systems, considering 1) investment in nature-based infrastructures for coastal defenses, 2) restoration-rehabilitation of natural (remnant) urban ecosystems and eco-engineering of current artificial infrastructures, focusing on reestablishment of biodiversity patterns and habitat connectivity, and 3) limitation of coastal town and village expansion. Management strategies can improve coastal adaptation to natural hazards, stabilizing changes in the natural-urban concatenation mosaic present in coastal urban systems like bays.