Protecting populations of native fish has been a key part of the Murray-Darling Basin Plan since it was implemented in 2012.
However, fish, fingerlings, eggs, larvae and other water life are being sucked into the thousands of irrigation pumps throughout the Murray-Darling river systems.
The Murray-Darling Basin Authority has found a standard 30-centimetre pipe sucked up about 240 fish a day.
With 4,546 irrigation pumps operating in New South Wales alone, up to 97 million fish are being lost each year.
An automatic screen solution is being trialled as an economic and environmental solution.
The screens are self-cleaning, low maintenance and low velocity, and are having received a mixed response.
Chief executive and founder of recreational fishing lobby group OzFish Unlimited, Craig Copeland, said new irrigation screens could be a game-changer for farmers and the environment.
"We have farmers who spend hours cleaning out their sprinkler heads or hours back-flushing their pumps," he said.
"With the new modern irrigation screens, they don't have to do that, so there is a big cost incentive and efficiency incentive for farmers — everyone wins."