Microbial risks and nutrient loading impacts of centralized treatment and converged wastewater discharge under dynamic coastal current

• Wastewater centralization and treatment upgrade reduced phosphorus and microbial pollution • Outfall relocation reshapes environmental gradient and microbial phenological response • Wet season induced elevated nitrogen loads by both wastewater discharge and land-based runoff • Hydrodynamics can mediate pathogen distributions and form localized microbial risk hotspots. • Spatiotemporal heterogeneity substantiates site-specific management to mitigate risks. Coastal ecosystems are increasingly affected by anthropogenic activities and land-based pollution, necessitating improved wastewater treatment systems and management strategies to ensure safe and sustainable usage. Using Victoria Harbor, Hong Kong as a model system, this study evaluates the ecological and water quality impacts of the combined centralizing and upgrading of preliminary wastewater treatment through contemporary monthly environmental DNA metabarcoding and long-term historical environmental monitoring data. Our findings indicate that while centralized chemically enhanced primary treatment significantly reduced phosphorus and microbial pollution in the study region when compared to historical baselines, the relocation of effluent discharge points reshaped microbial community structures in the direct effluent-receiving site VM7 with reduced Cyanobacteria. Beyond temperature as the seasonality indicator, parameters such as salinity, 5-day biological oxygen demand, and nitrite nitrogen were major contributors shaping the variation in microbial community composition. Under dynamic hydrodynamic conditions, VM7 could be a higher risk accumulation zone, enriching pathogens such as Bacteroides vulgatus . Temporally, elevated nitrogen concentration, particularly during the warm and wet season, were exacerbated by land runoff and rainfall-driven deposition, coinciding with increased pathogen prevalence. Seasonal analyses revealed that microbial activity and nutrient pollution were higher in the wet season, while key nitrogen transformation pathways, such as denitrification, decreased in the dry season. Comprehensive pathogen screening identified 27 potentially pathogenic bacterial species, predominantly at low abundances but with higher diversity at the effluent outfall. Notably, human pathogens increased during the wet season, raising health risks, although antibiotic resistance genes were not shown to be enriched. These results underscore the need for integrating spatial and temporal heterogeneity into environmental impact assessments to accurately capture risk dynamics. Emphasizing site-specific monitoring and management approaches is crucial for mitigating nutrient imbalances and microbial pollution, thus safeguarding coastal ecosystem health and public safety. This work provides essential insights for optimizing wastewater treatment and environmental management practices in coastal regions facing similar pollution challenges.