Average concentrations of nitrate in Malta’s groundwaters are probably the highest among EU member states. This compromises the quality of an important resource -almost 60% of Malta’s water supply being provided by groundwater. An 15N/14N + 18O/16O isotope study was undertaken as a core part of wide-ranging investigations into the potential sources of the nitrate pollution, its likely future trends, and possible ameliorative actions. The dual isotope (15N/14N + 18O/16O) approach was important for identifying waters affected by denitrification. Excluding these, groundwater from three physically and hydrologically distinct aquifers, with a very wide range in nitrate concentrations (24 to 410 mg NO3 L-1), had remarkably similar isotope compositions: 90% of samples lying within d15N ≈ +8 to +12‰, and d18O ≈ +3 to +6‰. The d18O values are entirely consistent with those expected for microbial nitrification in the presence of surface or groundwaters, and together with 15N values rule out nitrate derivation directly from fertilizers or sewage. In other studies the relatively high d15N values for the waters would probably have been interpreted as indicative of nitrate derived from manure. In Malta, however, cultivated soils have high d15N values, ≈ +6 to +11‰, very similar to the values for nitrate in the groundwater, and argue for a soil-derived source. The implications of a soil-source of such high nitrate levels are discussed, and the study emphasised the importance of characterising the compositions of soils in addition to other sources – a factor often neglected in isotope studies of nitrate