Stratification Controls Vertical Dynamics and Distribution of Organic Contaminants in Micro-Estuaries

Abstract Micro-estuaries receive elevated loads of organic contaminants, yet the influence of water-column structure on their vertical distribution remains unclear. We investigated contaminant dynamics in three structurally distinct micro-estuaries during the dry season using monthly water-column and sediment sampling. Across 63 samples, 274 organic contaminants were detected. Contaminant mixtures shifted seasonally from runoff-to baseflow-dominated conditions, transitioning from pesticide-dominated profiles to more persistent industrial and effluent-derived compounds, including PFAS and sucralose. Water-column stratification strongly influenced contaminant partitioning: strongly stratified systems showed surface accumulation, while well-mixed systems exhibited uniform vertical distributions. Intermediate systems displayed partial segregation, reflecting intermittent mixing and prolonged deep-water residence times. Sediment–deep water distribution coefficients did not correlate with the sediment organic carbon content, suggesting that the dynamic estuarine conditions prevent steady-state sorption–desorption equilibrium. These findings demonstrate that stratification shapes contaminant persistence and biological exposure, underscoring the need for monitoring and risk assessments that incorporate vertical structure.