Globally, dams and water extractions are well-recognised disruptors of flow regimes in floodplain wetlands, but little is known of the hydrological and ecological impacts of floodplain earthworks constructed for irrigation, flood mitigation and erosion control. We mapped the distribution of earthworks with high-resolution SPOT (Système Probatoire d'Observation de la Terre) imagery in an internationally recognised Ramsar wetland, the Macquarie Marshes of the Murray–Darling Basin, Australia. There were 339 km levees, 1648 km channels, 54 off-river storages and 664 tanks (0.5–5 m high), detected within the 4793 km2 floodplain study area. Earthworks reduced localised flooding compared with undeveloped sites. The most pronounced disconnection of the original floodplain (73.0%) occurred where earthworks were most concentrated compared with areas with few earthworks (53.2%). We investigated relationships between hydrological connectivity and mortality of the perennial flood-dependent river red gum Eucalyptus camaldulensis at 55 floodplain sites (225 × 150 m). Over half of the river red gums were dead at 21.8% of the sites. Earthworks blocked surface flows to flood-dependent vegetation and drowned vegetation in artificially inundated off-river storages. Mortality was due to impacts of earthworks and potentially exacerbated by effects of river regulation, water extraction and climate. River red gums were healthiest in narrow river corridors where earthworks confined flows and flows could recede freely. Rehabilitation of flood-dependent ecosystems should focus on reinstating lateral connectivity and protecting environmental flows. Copyright © 2011 John Wiley & Sons, Ltd.