Australian wetlands are important cultural sites and provide critical ecosystem services, including carbon sequestration and greenhouse gas abatement. However, these wetlands are easily degraded by non-native ungulates, such as feral pigs and buffalo, which reduces their ecosystem function. We tested for degradation from feral ungulates by measuring greenhouse gas emissions at disturbed and undisturbed wetland sites. Our samples were made in regions of cultural significance in northern Australia, over two seasons, using two measurement techniques and accounting for autotrophic respiration by plants. We consistently found that emissions of methane and nitrous oxide were meaningfully higher at disturbed sites, especially in wet soil conditions. For carbon dioxide, all sites were sinks, but the magnitude of the sink was reduced at disturbed sites. Our results provide novel and robust evidence of the impact of feral ungulate disturbance on greenhouse gas emissions in Australian wetlands. Management of wetland feral ungulates would deliver meaningful emissions abatement, but will require sustainable, long-term funding, which could be supported by income from new sources such as a proposed carbon crediting method.