A category 5 tropical cyclone swept a storm surge across remote Pukapuka Atoll in the Northern Cook Islands (South Pacific Ocean) in late February 2005. Groundwater salinity (specific conductance) observations are reported for the 2-year post-storm period, with the aim of investigating the effects of saltwater intrusion on thin freshwater lenses within the atoll islets. This is the first article to present field observations of such an event. Specific conductance at shallow depths increased dramatically from potable conditions (approximately 1,000 μS/cm) to brackish levels unsuitable for drinking (up to 10,000 μS/cm) shortly after the cyclone. Subsequently, the freshwater lenses required 11 months to recover. Within the thickest aquifer, a well-defined saline plume formed at 6 m depth, sandwiching a freshwater layer beneath it and the base of the lens. Plume dispersal proceeded only gradually, owing to its formation at the start of the SW Pacific regional dry season and the low tidal range on Pukapuka. Consequently, the remnant of the plume was still present 26 months after the saltwater incursion. An important finding was that the freshwater horizon preserved at depth maintained salinity levels below 1,800 μS/cm (i.e. within usable limits) for at least 5 months after surface overwash.