Extreme climate events are predicted to alter estuarine salinity gradients exposing habitat-forming species to more frequent salinity variations. The intensity and duration of these variations, rather than the mean salinity values ecosystems are exposed to, may be more important in influencing resilience but requires further investigation. Precipitation, including the frequency, intensity and timing of occurrence, is shifting due to climate change. A global analysis on the timing of rainfall in estuarine catchments was conducted. In 80% of the case studies, the maximum daily rainfall occurred in the dry season at least once over the 40-year period and could be classified as an extreme event. We selected an estuary in southwestern Australia and investigated the effects of an extreme rainfall event in 2017 resulting in an excess discharge of freshwater on seagrass Halophila ovalis. Adapting an approach applied for marine heatwaves using salinity data, we quantified metrics and characterised the event along the estuarine gradient. We assessed seagrass resilience by calculating resistance times based on the comparisons of biomass and leaf density data prior to, and during the event, and recovery times through assessment against historical condition. Where salinity is historically more variable, reductions in biomass were lower (higher resistance via plasticity in salinity tolerance) and meadows recovered within 9–11 months. Where salinity is historically more stable, loss of biomass was greatest (low resistance) post-event and recovery may exceed 22 months, and potentially due to the rapid decline in salinity (−3 PSU/day). As estuaries become more hydrologically variable, these metrics provide a baseline for retrospective and future comparisons. Our results suggest seagrass resilience to hyposalinity is population specific. This understanding enables more accurate predictions about ecological responses to climate change and identifies which populations may ‘future proof’ ecosystem resilience. Synthesis. Following an extreme rainfall event, we found seagrass populations that are exposed to variable salinities recovered while those from a stable salinity environment were unable to recover within the study time frame. These findings expand upon existing evidence, derived primarily from other ecosystems, that show new sources of resilience may be uncovered by accounting for between-population variation.