Coastal, freshwater wetlands in northern Australia are at risk of increased saltwater intrusion associated with sea-level rise, which threatens the persistence of numerous freshwater plant species by increasing salinity. Waterlilies (Nymphaea) are widespread in northern Australia, and their loss from these wetlands will be detrimental, both ecologically and culturally. This study aimed to define the regeneration tolerance of Nymphaea to increased salinity through quantifying the effects of salinity on seed germination and early seedling growth in four Nymphaea species. Seed germination and seedling growth were assessed under a gradient of salinity concentrations. Seeds that did not germinate after salinity exposure were assessed for their ability to recover in fresh water. For all species, there was a significant reduction in germination when seeds were exposed to salinities of ≥100 mM NaCl. Total seedling biomass was less sensitive to increasing salinity than germination, however declined significantly across all species at salinities ≥100 mM NaCl. Ungerminated seeds from all salinity treatments displayed some degree of recovery when transferred to fresh water. For the majority of species, however, seed germination of these transferred seeds never reached the percentages observed in the non-saline controls. For most species of Nymphaea, any salinization event reaching ≥100 mM NaCl will significantly reduce recruitment from seeds, irrespective of whether saline water is flushed from the system. The predicted future increases of saltwater intrusion into coastal freshwater wetlands in Northern Australia associated with global sea-level rise will likely result in significant habitat loss for many Nymphaea species.