Widespread and unprecedented drought across southern Australia over the past decade or more has greatly affected inland water ecosystem condition. Flooding since 2009 has broken the drought in the south-east of the continent, but the drought continued (as of early 2011) in the south-west There is substantial scientific evidence of a component of change towards a drier climate across southern Australia and a warmer climate nationally. Drier landscapes have the potential for increased rates of sedimentation due to decreased vegetative cover, exacerbated by the potential for more frequent and intense storms

Historical allocations of surface water and groundwater have changed the ecological character of many river and wetland systems across southern Australia; development pressures are generally much less in the northern half of the continent Recovery of water for increased environmental flows in the Murray–Darling and Snowy basins has reduced this pressure on some inland water ecosystems Most new water for Australian metropolitan areas will come from resources other than development of new inland resources—sources will include reuse and seawater desalination, improving run-off and recharge into existing infrastructures, and trading with existing users

For most of Australia, historical land clearing for dryland agriculture and locally intensive agricultural land uses continue to place river systems under pressure from nutrient run-off, sedimentation and salinisation The growth of the peri-urban fringe around major metropolitan areas places great pressure on local waterways and can involve the irreversible drainage of local wetlands Riparian degradation by livestock and feral pests is an ongoing impact

Vertebrate pests continue to impact most inland water systems across the continent, through grazing-related impacts, direct ecological competition or as a hazard to native predators (as in the case of cane toads) Waterway and floodplain weed infestations are widespread but of variable local impact