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These low-lying areas are vulnerable to impacts from tropical cyclone induced storm surges. The role of such surges on the long-term salinity of water resources, particularly the salinisation of drinking water ponds, a key water resource, requires further investigation. Here we show, using high-resolution measurements of pond hydrology and numerical modelling, that episodic inundation events cause the widespread salinisation of surface water and groundwater bodies in coastal areas. Sudden salt fluxes in ponds cause salinity build-up in the underlying sediments and become a source of salinity. Rapid clean-up of drinking ponds immediately after a surge event can significantly minimize these salinity impacts, which are likely to increase under climate change. 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