Coastal wetlands surrounding urban environments provide many important ecosystem services including protection from coastal erosion, soil carbon sequestration and habitat for marine and terrestrial fauna. Their persistence with sea-level rise depends upon their capacity to increase their soil surface elevation at a rate comparable to the rate of sea-level rise. Both sediment and organic matter from plant growth contribute to gains in soil surface elevation, but the importance of these components varies among sites and with variation in climate over long time scales, for which monitoring is seldom available. Here, we analysed variation in surface elevation, surface accretion and mangrove tree growth over 15 years in Moreton Bay, Queensland, Australia, a period that spans variation in the El Niño/La Niña (ENSO) cycle, which strongly influences rainfall and sea level in the region. Piecewise structural equation models were used to assess the effects of biotic (tree growth, plant cover and bioturbation by invertebrates) and environmental factors on annual surface elevation increments throughout this period. Our model for mangroves identified that surface accretion and tree growth were both positively influenced by rainfall, but surface elevation was not, and thus, higher levels of compaction of the soil profile in high rainfall/high sea level years were inferred. In contrast, our saltmarsh model found that rainfall positively influenced surface accretion and elevation gains. Declines in surface elevation in the mangroves were influenced by the species composition of the mangrove, with higher levels of elevation loss occurring in mangrove forests dominated by Avicennia marina compared to those with a higher proportion of Rhizophora stylosa. Decadal-scale variation in ENSO affected mangrove tree growth, but surface elevation trends were more strongly influenced by variation in environmental conditions than by tree growth, although effects of biotic factors (mangrove species composition and bioturbation) on surface elevation trends were observed. Further research into tipping points with extreme ENSO events (either La Niña with high rainfall and high sea level or El Niño with low rainfall and low sea levels) will help clarify the future of mangrove and saltmarsh distribution within Moreton Bay.