Despite offering welcome relief to the bushfire emergency and severe drought, widespread rain in the past fortnight has been a catalyst for more fish deaths, according to the Murray-Darling Basin Authority's latest drought update.
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The MDBA executive director of river operations, Andrew Reynolds, said it was a cruel twist, but an unavoidable risk that much-needed rain would contribute to fish deaths in areas affected by ash and sediment being washed into waterways.
"We have seen fish deaths in recent weeks in several locations under stress due to fires and the ongoing drought-in the Macquarie River, the Namoi, Gwydir, Border Rivers, Barwon-Darling, Lachlan, Upper Murray and Murrumbidgee rivers, and the Lower Darling continues to be an area of concern," he said.
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"Basin governments are on the ground working hard to relocate fish, install aerators and deliver strategic releases of water for the environment.
"Working with relevant state agencies, the MDBA is continuing to monitor the impacts on the Basin's water quality and quantity.
"The rain has so far had little impact on overall Basin storage levels, which are at 27 per cent capacity overall.
"Though some catchments will see levels recover slightly over coming weeks, the total volume of water in basin storages continued to decline over the past fortnight. We really need a long period of above-average rainfall to break current drought conditions."
Mr Reynolds said threats to water quality, most notably from algal blooms, would continue with reduced and no flows at many locations.
NSW sites with a blue-green algae red alert are the Wakool River at Stoney Crossing, Menindee Lakes at Lake Wetherell, Darling River at Louth, Bogan River at Gongolgon, Barwon River at Brewarrina, Namoi River downstream of Lake Keepit, Lake Cargelligo outlet, Burrendong Dam, Copeton Dam, Pindari Dam, Mehi River at Gundare, Macintyre River at Lake Inverell and the Macquarie River downstream of Burrendong Dam.