Concern for saline and microbial quality post-December 2004 tsunami, led to a field based surveillance study to systematically investigate the sanitary hazards which cause faecal contamination of groundwater. In seven islands, two duplicate sample sets, in two surveys, revealed that only 6.4% of the 173 well water samples (combining both surveys) satisfied the WHO Drinking Water Quality Guideline for 44˚C thermo-tolerant (Faecal) Coliform (FC) indicator value (zero cfu/100ml sample). Based on a combined risk analysis of Sanitary Hazard Score (SHS) and FC counts, more than 57.7% of the study wells were classified as at very high (FC: 100 to >1000 cfu/100ml; and SHS: ≥9) microbial health risk. During this study, fundamental changes were made to the published generic sanitary inspection method (WHO, 1997) for identifying sanitary hazards, for its application in the extremely vulnerable hydro-geological setting of the Maldives. However, the most important hazard controlling the intensity of faecal contamination in the Maldives is the safe separation distance between a latrine seepage point and the well. It was demonstrated that, due to the prevailing hydro-geological conditions and the well and sanitation system densities, safe separation distance cannot be achieved. Consequently, septic tank effluent quality must be greatly improved.