The freshwater resources of coral atolls occur mainly as lenses floating on salt water underneath the islands. The size and shape of these lenses are determined by hydrogeologic characteristics, the rainfall recharge rate and its temporal variation, plus extractions (Underwood et al., 1992; Jones and Banner, 2003; Jocson et al., 2002). In the South Pacific, rainfall exhibits seasonal as well as interannual variability related to the El Ni¿o-Southern Oscillation (ENSO) (Ropelewski and Halpert, 1987). We used electric conductivity measurements from pumped wells on Tongatapu to show a moderate ENSO control on the temporal fluctuation of the pumped freshwater salinity. The salinity dynamics depended on low or increased rainfall recharge during respectively dry El Ni¿o periods or wet La Ni¿a events. ENSO events cause a large variation around the mean salinity and determine the relative salinity over the time-scale of several years, while a smaller variation is introduced by seasonal rainfall. The Southern Oscillation Index (SOI) (Troup, 1965; Stone et al., 1996) was used to predict freshwater salinity with a lag time of 10 months.