The Giant dragonfly (Petalura gigantea) is an endangered species which is dependent on upland swamps for habitat. Nationally protected upland swamps are endangered ecological communities present in Sydney’s drinking water catchments and in surrounding areas. Giant dragonfly is a suitable umbrella species for the conservation of these upland swamps and their water dependent species. We investigated the risks associated with water extraction from upland swamp catchments, including through ‘incidental take’ associated with longwall mining induced subsidence. A conceptual lumped model was developed in python and calibrated using the observed discharge and groundwater storage data for three monitored swamps. Model results were interrogated to estimate the available Giant dragonfly habitat under different climatic conditions, and the relationship with the streamflow record was used to estimate the minimum flow percentile required for the maintenance of larval habitat. Our findings demonstrate the sensitivity of Giant dragonfly to water extraction, highlighting the need for improved water management to protect upland swamp environments and adhere to Australia’s national strategy for Ecologically Sustainable Development.