Tropical islands typically have limited access to safe water. In many cases, people in these communities source their drinking water from groundwater without quality evaluation and treatment. Thus, we determined the physico‐chemical and microbial characteristics of groundwater samples. Results showed substantial non‐compliance of parameters including microbial quality with the local and World Health Organization quality standards for drinking water. Significant seasonal differences were observed for turbidity, total iron (Fe), colour, hardness, Escherichia coli and total coliforms (n = 88; p < 0.0203), whereas the effect of elevation has moderate‐to‐strong correlations with pH (r = 0.73, p < 0.001), total dissolved solids and electrical conductivity (r > −0.65, p < 0.001). The microbial profile revealed elevated levels up to a detectable limit of 5000 CFU/100 mL of E. coli. Furthermore, 16S rRNA gene sequencing analysis identified a potentially new strain with a 98.5% similarity to Shigella flexneri, having the presence of multidrug‐resistant and virulent genes.

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