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Background: The chemical quality of drinking water is widely unknown in low-income countries. Objective: We conducted an exploratory study in Manhiça district (Mozambique) to evaluate drinking water quality using chemical analyses and cell-based assays. Methods: We measured nitrate, fluoride, metals, pesticides, disinfection by-products, and industrial organochlorinated chemicals, and conducted the bioassays Ames test for mutagenicity, micronuclei assay (MN-FACS), ER-CALUX, and antiAR-CALUX in 20 water samples from protected and unprotected sources. Results: Nitrate was present in all samples (median 7.5 mg/L). Manganese, cobalt, chromium, aluminium, and barium were present in 90–100% of the samples, with median values of 32, 0.6, 2.0, 61, 250 μg/l, respectively. Manganese was above 50 μg/l (EU guideline) in eight samples. Arsenic, lead, nickel, iron, and selenium median values were below the quantification limit. Antimony, cadmium, copper, mercury, zinc and silver were not present. Trihalomethanes, haloacetic acids, haloacetonitriles and haloketones were present in 5–28% samples at levels ≤4.6 μg/l. DDT, dieldrin, diuron, and pirimiphos-methyl were quantified in 2, 3, 3, and 1 sample, respectively (range 12–60 ng/L). Fluoride was present in one sample (0.11 mg/l). Trichloroethene and tetrachloroethene were not present. Samples were negative in the in vitro assays. Significance: Results suggest low exposure to chemicals, mutagenicity, genotoxicity and endocrine disruption through drinking water in Manhiça population. High concentration of manganese in some samples warrants confirmatory studies, given the potential link to impaired neurodevelopment.