The Murray–Darling Basin Authority (MDBA) head of environmental management, Carl Binning, said the 2015-16 survey, undertaken by the MDBA and basin states, caught more than 31,000 fish at 141 sites across the basin.
"The fish caught the most this year was a small native fish, the carp gudgeon—which is not to be confused with European carp, an introduced species that is harmful to native fish as they compete for food and habitat," Mr Binning said.
"Carp gudgeon measure about 30 millimetres and are an important food source of food for larger native fish, including golden perch and juvenile Murray cod.
"Murray cod were found in 19 of the 23 basin catchments. This is good news for the threatened species that were once widespread across the basin's tributaries," Mr Binning said.
"This year the largest Murray cod we measured was just over one metre and weighed in at 15 kilograms—a long way from the weight of those routinely caught last century weighing in at 100 kilograms.
"This shows that while we're on the right path, there is more work to be done to ensure improvements in fish populations under the Basin Plan.
"For example, we still haven't seen many changes in European carp numbers. In the 2015-16 survey we caught almost 1.3 tonnes of carp, which is slightly up from last year's survey when we removed 1.1 tonnes."
"Another introduced pest fish, the Gambusia, also known as the mosquito fish, was the second most caught fish."
Mr Binning said the survey was important in determining the contribution of Basin Plan measures for restoring fish health.
"The Murray–Darling Basin Plan is about ensuring a healthy and productive river system for future generations.
"When the Basin Plan was drafted, water extraction from the system had increased four-fold in 50 years—this was not sustainable for the environment or, in the long term, for the productive capacity of the Basin.
"It is important we balance the needs of community, industries and the environment—and have the evidence base to make decisions from.
"We need to maintain our 16 internationally significant wetlands as well as other habitat so the 35 endangered bird species, 16 endangered mammal species as well as the 46 species of native fish don't end up extinct.
"Over the next few months we will be further analysing the data we've collected so we can compare trends with river flows and environmental water delivery to inform the preliminary evaluation of the Basin Plan in 2017," Mr Binning said.
The MDBA's fish data is available online at http://data.gov.au/dataset/fish2014to2016.
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