Monitoring critical marine resources through non-invasive methods is essential for effective coastal management. Fish communities are vital components of coastal ecosystems, yet their biodiversity and assemblage structure face increasing threats from urbanization and intensified fishing pressure. This study utilized eDNA metabarcoding to assess territory-wide fish diversity, community composition, and environmental correlates across 16 sites in Hong Kong's highly urbanized estuarine-coastal waters. Our eDNA metabarcoding-based analysis identified 76 fish species, including commercially important and threatened taxa. Notably, fish diversity hotspots with high alpha diversity were found in the turbid western and central waters. Substantial overlap in species composition was observed between the western and central waters, as well as in the transition zones connecting these areas to the southern region. eDNA metabarcoding surveys exhibited distinct advantages in detecting fish species that are typically missed or underrepresented in convetional net-based trawl surveys, as reflected by the increased detection of small-sized, schooling, and elusive low-trophic-level fish taxa—particularly from Clupeiformes and Mugiliformes—in the current study. Environmental gradients, specifically salinity, total phosphorus, and chlorophyll a, had significant impacts on fish community dissimilarity. Co-occurrence network analysis identified putative keystone fish species, such as Sardinella melanura and Nibea coibor, underscoring their central roles in ecosystem stability. This study highlights the value of eDNA metabarcoding-based surveys for enhanced assessments of fish diversity, including rare and elusive low-trophic-level species, across complex estuarine gradients in urban coastal environments, thereby supporting effective coastal resource management.
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