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, as well as the rainfall recharge rate and its temporal variation, plus abstractions for domestic, industrial or agricultural use. Here we discuss the impact of agricultural activities as well as climatic variations on the quality of the freshwater lenses of Tongatapu, Kingdom of Tonga. Agriculture has strongly intensified since 1987 and nowadays it makes up over 50% of national export. We measured significant amounts of nitrates leaching out of the rootzone through the shallow volcanic soil and the karstic limestone towards the groundwater. In the South Pacific, rainfall exhibits seasonal variability, as well as inter-annual cycles, which themselves are related to the El Niņo-Southern Oscillation (ENSO). We show an ENSO control on the temporal pattern of the salinity of the lenses. We used electric conductivity measurements from pumped wells on Tongatapu to reveal the salinity fluctuations. The salinity dynamics depended on the pattern of low rainfall recharge during dry El Niņo periods, or dilution throughout wetter La Niņa events. These events then determine the quality of the freshwater lenses over the time-scale of several years, independent from seasonal rainfall patterns. We used the Southern Oscillation Index (SOI) to predict the salinity dynamics of the lenses using a lag period of 10 months. The soil is often shallow on these type of islands and provides the sole filter determining the transport of water and solutes. We discuss both agricultural and climatic impacts that should be considered for the sustainably management of the freshwater of small islands.