Hypoxic blackwater events occur worldwide, affecting inland and coastal waters. These events have been exacerbated by man‐made floodplain drainage, leading to large‐scale fish kills and ecological degradation. This paper presents a new method to identify estuarine catchment areas that are most likely to generate hypoxic conditions. The method uses established risk factors, including vegetation type, inundation extent and duration, ground‐truthed in eastern Australia. A catchment is at higher risk of hypoxic blackwater generation if (i) it is located where floodwaters are high and/or drainage is impeded, (ii) the site topography includes an extensive, low‐lying floodplain; and/or (iii) the land‐use and environmental characteristics have a high deoxygenation potential. Consequent impacts to an estuary are determined by the floodplain connectivity with the estuary, and the discharge characteristics of the catchment drainage system. Where multiple, proximate catchments have similar drainage conditions, compounding plumes of hypoxic blackwater can overwhelm the assimilation capacity of the estuary. Climate change may significantly increase the volume and frequency of blackwater events in estuarine environments as a result of reduced drainage due to sea level rise, higher temperatures, and more intense and sporadic rainfall events. It is recommended that management measures be introduced to mitigate the effects of climate change and avoid further widespread hypoxic blackwater events.This article is protected by copyright. All rights reserved.