Mangrove surface elevation was measured by means of the Surface Elevation Table and Marker Horizon technique (SET-MH) in a range of settings in southeastern Australia. Despite sustained vertical accretion, surface elevation declined at most sites with the onset of an El Niño drought in 2001–2002. At these sites, the Southern Oscillation Index accounted for 70–85% of variability in surface elevation over a 3-year period. At deltaic island sites, this trend was not evident, an observation we attribute to lower terrestrial groundwater inputs. At one site (Homebush Bay), a high correlation was found between surface elevation and groundwater depth, monitored approximately every 2 weeks for 4 months. At the same site, the diurnal astronomical tide was also found to significantly affect mangrove surface elevation, although not to the extent of the El Niño drought. Models of the response of mangroves to sea-level rise on the basis of contemporary processes should account for short-term perturbations, such as climate variability at regional and local scales.