Recent evidence indicates that climate change and intensification of the El Niño Southern Oscillation (ENSO) has increased variation in sea level. Although widespread impacts on intertidal ecosystems are anticipated to arise from the sea level seesaw associated with climate change, none have yet been demonstrated. Intertidal ecosystems, including mangrove forests are among those ecosystems that are highly vulnerable to sea level rise, but they may also be vulnerable to sea level variability and extreme low sea level events. During 16 years of monitoring of a mangrove forest in Mangrove Bay in north Western Australia, we documented two forest dieback events, the most recent one being coincident with the large-scale dieback of mangroves in the Gulf of Carpentaria in northern Australia. Diebacks in Mangrove Bay were coincident with periods of very low sea level, which were associated with increased soil salinization of 20-30% above pre-event levels, leading to canopy loss, reduced Normalized Difference Vegetation Index (NDVI) and reduced recruitment. Our study indicates that an intensification of ENSO will have negative effects on some mangrove forests in parts of the Indo-Pacific that will exacerbate other pressures.