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In a world where clean water is not just a necessity but a determinant of human health and socio-economic progress, many developing countries grapple with poor water quality, posing significant health risks and hindering development. This issue is particularly pronounced in (sub)tropical regions, where dynamic pathogen distribution in surface waters remains poorly understood. Breaking new ground, this study delves deep into the complexities of microbial water quality dynamics in a river in Bangladesh. For the first time, the study quantifies and combines the impacts of socio-economic and climate change on microbial water quality. Key findings reveal a nuanced picture: while climate change does influence water quality, socio-economic factors—population growth, urbanization, and inadequate wastewater treatment—have a more significant impact. What sets this study apart is its innovative scenario analysis, projecting future microbial water quality based on socio-economic and climate change variables. The results underscore the urgent need for targeted interventions, particularly in wastewater treatment and sanitation, to mitigate contamination and improve water quality. The study's findings offer valuable insights for water managers and policy makers, providing a basis for formulating strategies to reduce widespread faecal contamination and mitigate waterborne disease outbreaks. The developed model serves as an ideal tool for quantifying the future influence of climate change and socio-economic developments on FIB fate, transport, and dynamics. The methodology and findings are likely applicable beyond Bangladesh, serving as a valuable reference for regions facing similar challenges. In conclusion, this groundbreaking study illuminates the intricate interplay between climate, socio-economic factors, and water quality in developing countries. It offers valuable tools and insights for policymakers, water managers, and researchers striving to improve water quality and public health. By addressing both environmental and human factors, the study paves the way for comprehensive strategies to ensure clean water access and enhance the quality of life for millions.