Abstract
This study presents a holistic assessment of anthropogenic pollution in three rivers of Sri Lanka, Gin Ganga (G), Kepu Ela (K), and Moragoda Ela (M) through integrated land use mapping, physicochemical analysis, 16S rRNA sequencing, quantitative PCR for antibiotic resistance genes (ARGs; mphA, blaIMP), and quantitative microbial risk assessment (QMRA). Land use analysis identified the highly urbanized M River catchment as the most impacted, exhibiting elevated levels of Escherichia coli, chemical oxygen demand (COD), and electrical conductivity (EC) compared to less urbanized rivers. A key finding was the effect of seawater intrusion (SWI) at the M4 sampling site, where extreme EC (up to 6330 µS/cm) reduced culturable E. coli but increased Bacteroidales, suggesting the latter’s potential as a more reliable fecal indicator in brackish environments. SWI also simplified microbial community structure, favoring stress-tolerant bacterial species. Multiple regression analysis of ARG fluctuations revealed that COD and EC emerged as strong, significant predictors for mphA, directly linking it to wastewater, while blaIMP was widespread irrespective of urbanization. Stochastic QMRA using Monte Carlo simulation with bootstrap concentration uncertainty quantified annual infection risks for agricultural users, expressed as Disability-Adjusted Life Years (DALY) per person per year. M River exhibited the highest annual DALY per person per year with a mean of 1.69×10⁻⁶, and a WHO guideline exceedance rate of 100% while K and G rivers were under WHO threshold with a 0% exceedance rate. Reclaimed water (sourced from a tertiary wastewater treatment facility in Sapporo, Japan, where 100% of the river flow is treated wastewater used for recreation) emerged as the safest option with a mean DALY per person per year of 1.17×10⁻⁸, a 0% exceedance rate, and the largest safety margin relative to the tolerable risk threshold indicating a timely need in using reclaimed water for irrigation. These findings highlight how urban wastewater discharge combined with SWI can distort conventional water quality indicators, alter microbial ecology, and elevate public health risks when using for irrigation. We advocate improved wastewater treatment, adoption of salinity-resilient microbial indicators than conventional indicators, and expanded use of reclaimed water to enhance water safety in tropical coastal cities.