By 2100, it is predicted that streams in the Kakadu region in Northern Australia will be transforming in their coastal floodplains to saline environments because of sea-level rise. Potential impacts need to be assessed, together with existing threats, to manage future change. The fish and macroinvertebrate assemblages of the streams in the region are well researched and were used as indicators to assess centennial-scale changes to freshwaters. Spatial and temporal patterns in assemblage dynamics were described using data from different habitat types, and used as a framework to review current knowledge and assemblage vulnerability for likely conditions ≥100 years from present-day. Twenty threats within three broad classes were identified (climate change, invasive species, decommissioning and rehabilitation of Ranger uranium mine). Seven threatening processes were ranked as high risk to catchment-scale distributions of fish and macroinvertebrate taxa, with six being associated with climate change and one with mine-site rehabilitation. Habitat connectivities and dependencies were identified as key ecological processes for both groups, with saltwater intrusion to coastal floodplains being identified as the major process that will alter assemblage dynamics and system energy flow. Risks posed by climate change highlighted priority research and monitoring needs for management and protection of upland freshwater-refuge habitats.
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