Runoff from acid-sulfate soils (ASS) is increasingly threatening the structure and function of estuarine ecosystems worldwide. Along the eastern coast of Australia, sulfuric acid is known to affect the growth and survival of mangrove saplings; however, impacts of ASS runoff on the structure and function of established mangrove trees are unclear. Pneumatophores, the aerial roots produced by some species of mangrove, are critical sites of gas exchange, allowing these species to persist in waterlogged soils. They also provide physical structure in estuarine sediments, facilitating communities of algae, invertebrates and, at high tide, fish. We tested the hypotheses that Avicennia marina (Forsk.) Vierh. pneumatophores would be less abundant, shorter, thinner and weaker close to major ASS outflow drains. Sampling at sites close to and away from drains within each of two estuaries of New South Wales, Australia, showed no effect of exposure to runoff on pneumatophore density or thickness. Pneumatophores were, however, shorter (∼2 cm) and weaker (up to two-fold) at ASS-affected than reference sites. Although the reduced length and strength of pneumatophores at acidified sites may limit the number of epifaunal molluscs they can support, the persistence of dense pneumatophores indicates that the capacity to benefit invertebrates and fish remains.