Zooplankton have been used widely to monitor and assess water quality and the impacts of various forms of pollution, including acidification, eutrophication, pesticides, algal toxins and climate warming. They are sensitive to changes in water quality such as temperature, nutrients, and organic matter, as well as changes in hydro-geomorphic conditions. The indicators of ecosystem health include abundance, biomass, composition, reproduction, species diversity, and functional diversity. To improve understanding of inland river health, we are currently developing the use of zooplankton in the context of the Darling-Baaka River, one of the major inland rivers of Australia. An initial analysis showed that “community index” was significantly related to algal biomass of the river, showing that zooplankton community was dominated by small forms such as protozoans and rotifers where algal blooms developed, which is a sign of a stressed system. This provides water managers with additional information on the biological assessment of inland river health.