Murray cod and crayfish are suffocating and jumping out of the river gasping for clean air in a phenomenon known as hypoxic blackwater, where oxygen levels drop due to bacteria sucking oxygen from polluted floodwaters.

Major flooding is still occurring at Echuca-Moama and other Victorian-NSW border towns after the Murray River peaked at record levels in October.

Recreational fishing charity OzFish has deployed an emergency team to rescue the fish in partnership with state fishing regulators and the Murray Darling Basin Authority.

OzFish founder and chief executive Craig Copeland said groups had rescued 250 freshwater crayfish at Barham this week and been deployed at Nyah and Swan Hill.

"Co-ordinating these collaborative rescue efforts is vitally important and we are proud to be playing a part alongside so many like-minded and committed individuals and their organisations," he said in a statement on Friday.

"Given the situation affecting native fish we have a further Fish Emergency Recovery Team deploying from today to relocate as many native fish, including Murray cod, to safe water."

OzFish says the public shouldn't pick up or interfere with any distressed fish they encounter.

Instead, notify the charity, it says.

"Indicators of stress in native fish include discolouration, gasping for air and appearing at the water's surface," Mr Copeland said.

A Bureau of Meteorology update on Friday said rainfall in October was the highest on record for large parts of the Murray-Darling Basin.

Australian Associated Press