There are two lakes at the terminal of the Murray Darling Basin, Lake Alexandrina and Lake Albert. Historically these lakes were estuarine and had complete connection to the Coorong and Murray Mouth. Barrages were built in 1940 to stop salt water incursion into the lakes and upstream into the River Murray during periods of low flow. The barrages drastically altered the ecology of the lakes which typically have been maintained at full pool level. As a result of a drought in 2006, and over-allocation of water to upstream irrigators, the lakes are now facing significant pressure including no environmental water allocation, significant lake drawdown and salinization. Sea water leaking through the barrages is threatening industries that rely on water from the lake including stock watering and irrigation, and salinity is at concentrations high enough to compromise the health of the freshwater macrophytes. Plans to construct a temporary weir at the entrance to the lake are well advanced to ensure the supply to Adelaide city is secure and halt salt water incursion into the river channel. The lower River Murray lakes have experienced water quality problems, such as toxic cyanobacteria in the past, but the latest drought may irreversibly change the character of the lakes and there are genuine concerns for native fisheries, commercial fisheries and bird habitat.
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