Water contamination by micropollutants is a global issue, yet there is limited information from low-income regions. To address this, we evaluated surface water quality in rapidly growing sub-Saharan area of Malawi lacking wastewater treatment. Integrated assessment of passive sample extracts representing wet and dry seasons combined effect-based approach with in vitro bioassays, target and non-target chemical analyses (NTS). It revealed specific contamination profiles characterized by high concentrations of numerous pollutants, frequent exceedances of Predicted No-Effect Concentrations, and concerning levels of certain insecticides (chlorpyrifos, pirimiphos-methyl) and pharmaceuticals (sulfamethoxazole, trimethoprim, diclofenac). Proposed threshold values were exceeded for estrogenicity, androgenicity, aryl hydrocarbon receptor-mediated activity, thyroid hormone receptor agonism, and transthyretin (TTR) binding inhibition (highest effect-based trigger value exceedance, over 600-fold), which indicates risks to aquatic life. The combination of TTR pull-down assay, NTS, and bioassays enabled the isolation and identification of active compounds, including previously unreported TTR ligands 4-hydroxychlorothalonil (pesticide metabolite) and chlorothiazide (diuretic). Linear alkylbenzene sulfonates and related features contributed most significantly to TTR binding inhibition. This study introduces novel analytical approaches to address challenging groups of surfactants occurring in technical mixtures containing multiple branched isomers. The results underscore the added value of implementing effect-based assessment in understudied regions and the challenges posed by transformation products and technical mixtures lacking standards and reference spectra in NTS libraries. Our findings emphasize the need to expand MS/MS spectral libraries by incorporating metabolites and transformation products. The study highlights the impacts and risks of untreated wastewater discharges in regions affected by climatic and socio-economic pressures.