Sources, contamination pathways, and monitoring of pathogens in urban estuaries

Urban estuaries are critical ecological and socio-economic interfaces but are increasingly impacted by microbial pathogen contamination driven by anthropogenic activities such as wastewater discharge, stormwater runoff, agriculture, and wildlife inputs. Despite extensive documentation of estuarine pathogens, effective risk assessment and management remain constrained by key knowledge gaps related to source apportionment, environmental fate, and monitoring relevance. This review synthesizes current understanding of pathogen sources and transmission pathways in urban estuaries and critically examines the physicochemical, hydrodynamic, and sediment-mediated processes that regulate pathogen persistence, redistribution, and exposure risk. We identify three interconnected challenges: (i) limited resolution in differentiating human and non-human contamination sources due to overlapping microbial signatures; (ii) inadequate incorporation of estuarine hydrodynamics and sediment reservoirs into fate-and-transport frameworks; and (iii) misalignment between conventional monitoring indicators and actual pathogen and antimicrobial resistance risks. Emerging approaches, including microbial source tracking, sequencing-based surveillance, biosensors, and hybrid predictive modelling, are evaluated for their capacity to support risk-relevant decision-making. Framed within a One Health perspective, this review integrates microbial ecology, environmental processes, and surveillance technologies to support evidence-based management and sustainable mitigation of pathogen risks in urban estuaries.