The maintenance of soil surface elevation in mangroves supports the persistence of mangroves with sea level rise. Using surface elevation table (SET) methods we assessed the role of rainfall and associated river discharge in moderating surface elevation in mangroves of the Daintree River, Queensland, Australia. In sites in the main river channel close to the river mouth, increases in soil surface elevation were episodic with river flooding leading to greater accretion of sediment and increases in surface elevation in years with high river discharge, while in the tidal channel further from the mouth sediment accretion and surface elevation increments were variable among years and not linked to river discharge. Our study finds that the mangroves of the Daintree River estuary have surface elevation gains that are variable but similar to current rates of sea level rise through trapping of around 40,000 tonnes of sediment annually, mainly within the downstream mangroves and those in the main river channel. Extreme rainfall and river flows have spatially variable influences on surface elevation in mangroves which may lead to similarly variable responses to accelerating sea level rise.