Groundwater is an important source of water for coastal communities in Pacific Islands Countries. This study assessed the prevalence and predictors of faecal contamination in groundwater sources across 11 islands in Vanuatu. Escherichia coli was detected in 49% of sources and E. coli concentration exceeded 10 most probable number (MPN)/100 mL for 23% of sources. When adjusting for other variables, the detection of E. coli was significantly associated with severe pump stand corrosion, suggestive of contaminated run-off directly entering boreholes. E. coli concentration >10 MPN/100 mL was also significantly associated with (i) hand-dug wells (as compared to drilled boreholes); (ii) handpumps with severe pump stand corrosion; (iii) water points underlain by a volcanic geological formation (as compared to coral limestone); and (iv) rainfall in the previous 24 h. Encasing pump stands in concrete – as some communities had done – was found to have a significant protective effect. While baseline statistics for Sustainable Development Goal target 6.1 suggest that 87% of Vanuatu's rural population have access to at least a basic (improved) water source, the results from this study point to extensive microbial water quality concerns linked to degraded water supply infrastructure in need of rehabilitation.