Over 24 million hectares of the world's coastal floodplains are underlain by acid sulfate soils (ASS). Drainage of these sediments has led to widespread environmental degradation, raising serious health concerns. To date, onsite rehabilitation has been complicated by differing stakeholder priorities, with resources often allocated to sites with more vocal proponents rather than those exposed to more significant environmental impacts. To address this issue, this paper introduces the Coastal Floodplain Prioritisation (CFP) Method; a novel, data driven and spatially explicit multi-criteria assessment that ranks floodplain catchment areas according to their risk of transferring acidic drainage waters to an estuary. Results can be used to prioritise where remediation actions are likely to have the greatest benefit. The method was applied across six different estuaries in south-east Australia, with major field campaigns undertaken at each site. Within each estuary, the largest acid fluxes and impacts are identified with relevant mitigation measures provided. On a catchment scale, the results reflect the broader hydrogeomorphic characteristics of each estuary, including the historic acid formation conditions and recent anthropogenic drainage activities. Low-lying backswamps were identified as the highest risk zones within each estuary. These areas are also the most vulnerable to sea level rise. Reinstatement of tidal inundation to these backswamps effectively remediates acid sulfate soil discharges and provides a nature-based solution for adaptation to sea level rise with a range of co-benefits to encourage further investment.