Pollution and Anthropogenic Stressors Are Associate with Cetacean Vulnerability in Coastal Waters: Fine-Scale Diagnostics from eDNA and Multispecies Modeling

Indo-Pacific humpback dolphin (Sousa chinensis) and finless porpoise (Neophocaena phocaenoides) are increasingly threatened across their native range, yet the relative influence of multiple stressors in shaping their population dynamics remains unclear. Current conservation strategies for both species are limited by incomplete data and limited assessment of affecting factors. Here, we integrated eDNA metabarcoding with Joint Species Distribution Modeling (JSDM) to assess how environmental gradients, pollution, and trophic associations interactively influence cetacean distributions in Hong Kong waters. We show that degraded water quality and intensified human activity negatively associated with cetacean occurrence, with clear species-specific responses to different stressors. S. chinensis covaried most strongly with Secchi disc depth, and presence of vessels, while N. phocaenoides was negatively associated with nitrate nitrogen and microbial pollution (sewage). The JSDM variance partitioning analysis highlighted that the occurrence of S. chinensis was primarily associated with anthropogenic disturbances (30.04%), followed by water physical properties (26.63%), whereas N. phocaenoides was more strongly associated with physical (40.9%) and anthropogenic disturbances (35.2%). By integrating eDNA and JSDM, our approach provides fine-scale diagnostics of species-specific vulnerabilities, supporting adaptive conservation strategies and guiding the realignment of protected areas to mitigate biodiversity loss in urbanized marine ecosystems. Environmental ImplicationOur study demonstrates that hazardous water pollutants, including microbial contamination, nutrient enrichment, and chemical stressors, vessel pressure, show strong, species-specific impacts on resident cetaceans in Hong Kong. By integrating eDNA metabarcoding with joint species distribution models, we provide a diagnostic framework that directly links pollutant profiles to ecological risk. These findings highlight that conventional conservation strategies overlooking pollution drivers are insufficient for marine megafauna persistence. Our approach offers an early-warning system for monitoring hazardous pollutants in coastal ecosystems and supports adaptive management strategies to mitigate biodiversity loss in urbanized seascapes.