Abstract

Coastal aquatic ecosystems are highly dynamic and influenced by multiple natural and anthropogenic factors that can contribute to their degradation. In this study, we present an innovative and interdisciplinary approach that integrates the analysis of the physicochemical properties, metal concentrations, and microbial communities in the San Antonio River and Petrel Lagoon, located in Central Chile, to evaluate the ecological health of this coastal ecosystem. Nutrient concentrations, in particular NO3- (values ranged from 26.6 +/- 0.0 and 37.6 +/- 9.4 mg/L) and PO42- (values > 8.0 mg/L), were elevated upstream, reflecting agricultural inputs, while microbial indicators (E. coli) surpassed regulatory thresholds (>1,000MPN/100 ml) in several sites. Metal analyses revealed high Na and Mg, concentrations (>2,000 mg/L and > 280 mg/L, respectively) in waters and in Al, Fe and Li in sediments (values ranged from 20,000 to 1.0x10(6) mg/kg). Microbial community analyses in waters identified that most of the sites were dominated by Idiomarinaceae (16 % of total community) and Marinicella (5 % of total community), and with enrichment in Owenweeksia (12 % of total community) in downstream sites. Potential pathogenic genera, including Cutibacterium acnes, were detected, suggesting risks to water quality and public health. Multivariate analyses revealed spatial structuring driven by salinity and nutrient inputs, emphasizing the influence of hydrodynamics and land use. These findings highlight significant environmental gradients and contamination hotspots, stressing the need for a comprehensive approach that integrates a similar approach to better understand microbial dynamics, metal behavior, and their combined impact on water quality. Future studies should aim to overcome the limitations of this work in order to identify relevant indicators and develop effective monitoring strategies that support the sustainability of ecosystem services.